Starting phenix.real_space_refine on Mon Feb 19 17:06:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu9_29456/02_2024/8fu9_29456_neut.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16091 2.51 5 N 4185 2.21 5 O 4923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 558": "OD1" <-> "OD2" Residue "C PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25313 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8265 Classifications: {'peptide': 1058} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "B" Number of atoms: 8262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'CIS': 5, 'PTRANS': 54, 'TRANS': 997} Chain breaks: 3 Chain: "C" Number of atoms: 8254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8254 Classifications: {'peptide': 1056} Link IDs: {'CIS': 6, 'PTRANS': 54, 'TRANS': 995} Chain breaks: 3 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.62, per 1000 atoms: 0.54 Number of scatterers: 25313 At special positions: 0 Unit cell: (143.971, 179.755, 160.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4923 8.00 N 4185 7.00 C 16091 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 109 " " NAG A1202 " - " ASN A 262 " " NAG A1203 " - " ASN A 689 " " NAG A1204 " - " ASN A 697 " " NAG A1205 " - " ASN A 781 " " NAG A1206 " - " ASN A1054 " " NAG A1207 " - " ASN A1078 " " NAG A1208 " - " ASN A1114 " " NAG A1209 " - " ASN A 637 " " NAG A1210 " - " ASN A 583 " " NAG A1211 " - " ASN A 61 " " NAG A1212 " - " ASN A 596 " " NAG A1213 " - " ASN A 311 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 262 " " NAG B1203 " - " ASN B 596 " " NAG B1204 " - " ASN B 689 " " NAG B1205 " - " ASN B1054 " " NAG B1206 " - " ASN B 697 " " NAG B1207 " - " ASN B1078 " " NAG B1208 " - " ASN B1114 " " NAG B1209 " - " ASN B 637 " " NAG B1210 " - " ASN B 781 " " NAG B1211 " - " ASN B 583 " " NAG B1212 " - " ASN B 311 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 262 " " NAG C1203 " - " ASN C 596 " " NAG C1204 " - " ASN C 689 " " NAG C1205 " - " ASN C 697 " " NAG C1206 " - " ASN C 781 " " NAG C1207 " - " ASN C1054 " " NAG C1208 " - " ASN C1114 " " NAG C1209 " - " ASN C 323 " " NAG C1210 " - " ASN C 637 " " NAG C1211 " - " ASN C1078 " " NAG C1212 " - " ASN C 583 " " NAG C1213 " - " ASN C 311 " Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 4.8 seconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 41 sheets defined 23.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.338A pdb=" N LYS A 424 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 724 Processing helix chain 'A' and resid 726 through 734 removed outlier: 4.229A pdb=" N LEU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 763 removed outlier: 3.787A pdb=" N ASP A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 846 through 864 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 899 through 919 Processing helix chain 'A' and resid 921 through 924 Processing helix chain 'A' and resid 925 through 945 removed outlier: 4.015A pdb=" N VAL A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 948 No H-bonds generated for 'chain 'A' and resid 946 through 948' Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 965 through 1013 removed outlier: 4.857A pdb=" N VAL A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1126 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 717 through 723 Processing helix chain 'B' and resid 726 through 734 Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 738 through 762 removed outlier: 3.971A pdb=" N ASP B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 846 through 865 Processing helix chain 'B' and resid 866 through 870 Processing helix chain 'B' and resid 877 through 888 Processing helix chain 'B' and resid 892 through 898 removed outlier: 4.299A pdb=" N LEU B 896 " --> pdb=" O THR B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 920 removed outlier: 3.695A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 915 " --> pdb=" O ILE B 911 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 916 " --> pdb=" O GLY B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 945 Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 965 through 1013 removed outlier: 3.737A pdb=" N GLN B 972 " --> pdb=" O GLU B 968 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 726 through 734 Processing helix chain 'C' and resid 735 through 737 No H-bonds generated for 'chain 'C' and resid 735 through 737' Processing helix chain 'C' and resid 738 through 763 removed outlier: 4.099A pdb=" N ASN C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 806 Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 866 through 870 Processing helix chain 'C' and resid 877 through 888 Processing helix chain 'C' and resid 892 through 899 removed outlier: 4.387A pdb=" N LEU C 896 " --> pdb=" O THR C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 913 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 921 through 924 Processing helix chain 'C' and resid 925 through 945 removed outlier: 3.862A pdb=" N VAL C 931 " --> pdb=" O LYS C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 964 Processing helix chain 'C' and resid 965 through 1013 removed outlier: 4.330A pdb=" N VAL C 971 " --> pdb=" O PRO C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1125 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.754A pdb=" N HIS A 194 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ALA A 209 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N PHE A 207 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.500A pdb=" N VAL A 47 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 267 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 299 removed outlier: 5.341A pdb=" N ILE A 292 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 579 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN A 294 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 577 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A 574 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 308 removed outlier: 6.160A pdb=" N GLU A 304 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASN A 522 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 306 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.964A pdb=" N VAL A 375 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN A 374 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 496 " --> pdb=" O ASN A 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.690A pdb=" N CYS A 341 " --> pdb=" O CYS A 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA9, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.620A pdb=" N ILE A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 681 through 684 removed outlier: 6.698A pdb=" N ALA A 681 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS B 770 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN A 683 " --> pdb=" O LYS B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.442A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER A1035 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1041 " --> pdb=" O PRO A1033 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A1043 " --> pdb=" O SER A1031 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER A1031 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A1045 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 691 through 708 removed outlier: 6.442A pdb=" N SER A 691 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A1056 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 693 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1054 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A1052 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A1058 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A1075 " --> pdb=" O ALA A1058 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 716 removed outlier: 4.238A pdb=" N LYS A 713 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 767 through 770 Processing sheet with id=AB6, first strand: chain 'A' and resid 1100 through 1102 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.902A pdb=" N ILE B 190 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.581A pdb=" N ASP B 267 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 93 removed outlier: 4.462A pdb=" N GLY B 90 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 228 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 299 removed outlier: 5.278A pdb=" N ILE B 292 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 579 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLN B 294 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 577 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 296 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY B 574 " --> pdb=" O GLN B 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 334 through 338 Processing sheet with id=AC3, first strand: chain 'B' and resid 341 through 342 removed outlier: 6.808A pdb=" N CYS B 341 " --> pdb=" O CYS B 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 518 through 523 removed outlier: 5.442A pdb=" N ASP B 554 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 555 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE B 545 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 634 through 640 removed outlier: 5.158A pdb=" N THR B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 638 " --> pdb=" O THR B 676 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 681 through 684 removed outlier: 6.861A pdb=" N ALA B 681 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS C 770 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN B 683 " --> pdb=" O LYS C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.595A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B1047 " --> pdb=" O HIS B1028 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N HIS B1028 " --> pdb=" O TYR B1047 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 691 through 708 removed outlier: 6.595A pdb=" N SER B 691 " --> pdb=" O THR B1056 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR B1056 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 693 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN B1054 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B1052 " --> pdb=" O PRO B 695 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B1086 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B1091 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 713 through 716 removed outlier: 4.267A pdb=" N LYS B 713 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1100 through 1105 removed outlier: 4.863A pdb=" N ALA B1067 " --> pdb=" O SER B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.723A pdb=" N GLU C 211 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N HIS C 194 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N ALA C 209 " --> pdb=" O HIS C 194 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 36 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 52 removed outlier: 7.826A pdb=" N THR C 254 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP C 270 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 256 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA C 268 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 258 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AD5, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AD6, first strand: chain 'C' and resid 291 through 299 removed outlier: 5.224A pdb=" N ILE C 292 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR C 579 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN C 294 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 577 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 574 " --> pdb=" O GLN C 593 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 304 through 308 removed outlier: 4.417A pdb=" N GLU C 304 " --> pdb=" O CYS C 518 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 334 through 338 removed outlier: 4.068A pdb=" N VAL C 375 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN C 374 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 496 " --> pdb=" O ASN C 374 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 342 removed outlier: 6.476A pdb=" N CYS C 341 " --> pdb=" O CYS C 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.764A pdb=" N ILE C 650 " --> pdb=" O ILE C 646 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.417A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C1047 " --> pdb=" O HIS C1028 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N HIS C1028 " --> pdb=" O TYR C1047 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 691 through 708 removed outlier: 6.417A pdb=" N SER C 691 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C1056 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 693 " --> pdb=" O ASN C1054 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C1054 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU C1052 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C1058 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE C1075 " --> pdb=" O ALA C1058 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 713 through 716 removed outlier: 4.208A pdb=" N LYS C 713 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1100 through 1105 removed outlier: 5.599A pdb=" N ALA C1067 " --> pdb=" O SER C1103 " (cutoff:3.500A) 939 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.94 Time building geometry restraints manager: 9.64 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: 4526 1.32 - 1.44: 6776 1.44 - 1.57: 14400 1.57 - 1.70: 36 1.70 - 1.82: 145 Bond restraints: 25883 Sorted by residual: bond pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " ideal model delta sigma weight residual 1.516 1.726 -0.210 2.50e-02 1.60e+03 7.06e+01 bond pdb=" N PRO C 487 " pdb=" CA PRO C 487 " ideal model delta sigma weight residual 1.473 1.442 0.031 8.50e-03 1.38e+04 1.33e+01 bond pdb=" CB ASN C 894 " pdb=" CG ASN C 894 " ideal model delta sigma weight residual 1.516 1.427 0.089 2.50e-02 1.60e+03 1.27e+01 bond pdb=" CB LEU B 808 " pdb=" CG LEU B 808 " ideal model delta sigma weight residual 1.530 1.598 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CB LEU B1125 " pdb=" CG LEU B1125 " ideal model delta sigma weight residual 1.530 1.596 -0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 25878 not shown) Histogram of bond angle deviations from ideal: 74.74 - 86.60: 2 86.60 - 98.46: 1 98.46 - 110.32: 7282 110.32 - 122.18: 23085 122.18 - 134.04: 4854 Bond angle restraints: 35224 Sorted by residual: angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" OD1 ASN A 689 " ideal model delta sigma weight residual 120.80 74.74 46.06 2.00e+00 2.50e-01 5.30e+02 angle pdb=" CB ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 116.40 85.25 31.15 1.50e+00 4.44e-01 4.31e+02 angle pdb=" OD1 ASN A 689 " pdb=" CG ASN A 689 " pdb=" ND2 ASN A 689 " ideal model delta sigma weight residual 122.60 131.81 -9.21 1.00e+00 1.00e+00 8.48e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.23 -6.57 7.20e-01 1.93e+00 8.34e+01 angle pdb=" C GLU A 211 " pdb=" N PRO A 212 " pdb=" CA PRO A 212 " ideal model delta sigma weight residual 119.85 128.39 -8.54 1.01e+00 9.80e-01 7.15e+01 ... (remaining 35219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15229 17.71 - 35.42: 434 35.42 - 53.13: 98 53.13 - 70.85: 61 70.85 - 88.56: 28 Dihedral angle restraints: 15850 sinusoidal: 6615 harmonic: 9235 Sorted by residual: dihedral pdb=" CA THR B 921 " pdb=" C THR B 921 " pdb=" N PRO B 922 " pdb=" CA PRO B 922 " ideal model delta harmonic sigma weight residual -180.00 -143.46 -36.54 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA ASP B1119 " pdb=" C ASP B1119 " pdb=" N PRO B1120 " pdb=" CA PRO B1120 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N ILE A 106 " pdb=" CA ILE A 106 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 15847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3122 0.079 - 0.157: 766 0.157 - 0.236: 146 0.236 - 0.314: 39 0.314 - 0.393: 21 Chirality restraints: 4094 Sorted by residual: chirality pdb=" C2 NAG B1201 " pdb=" C1 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" N2 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2 NAG B1203 " pdb=" C1 NAG B1203 " pdb=" C3 NAG B1203 " pdb=" N2 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1 NAG A1213 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG A1213 " pdb=" O5 NAG A1213 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4091 not shown) Planarity restraints: 4573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 pdb=" C1 NAG A1203 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 689 " 0.029 2.00e-02 2.50e+03 2.06e-01 4.25e+02 pdb=" CG ASN A 689 " 0.326 2.00e-02 2.50e+03 pdb=" OD1 ASN A 689 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 689 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 596 " 0.048 2.00e-02 2.50e+03 4.84e-02 2.93e+01 pdb=" CG ASN B 596 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 596 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 596 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1203 " 0.058 2.00e-02 2.50e+03 ... (remaining 4570 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5455 2.77 - 3.30: 23088 3.30 - 3.84: 40859 3.84 - 4.37: 48951 4.37 - 4.90: 81155 Nonbonded interactions: 199508 Sorted by model distance: nonbonded pdb=" OG1 THR C 33 " pdb=" O PRO C 204 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.280 2.440 nonbonded pdb=" N ASN A 689 " pdb=" OD1 ASN A 689 " model vdw 2.333 2.520 nonbonded pdb=" OG SER C 864 " pdb=" OG1 THR C 867 " model vdw 2.345 2.440 nonbonded pdb=" OG SER A1103 " pdb=" N GLY A1104 " model vdw 2.353 2.520 ... (remaining 199503 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 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) selection = (chain 'B' and (resid 14 through 807 or resid 834 through 1125 or resid 1201 thr \ ough 1212)) selection = (chain 'C' and (resid 14 through 601 or resid 621 through 1125 or resid 1202 thr \ ough 1213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.920 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 67.670 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.210 25883 Z= 0.780 Angle : 1.348 46.062 35224 Z= 0.897 Chirality : 0.077 0.393 4094 Planarity : 0.006 0.206 4535 Dihedral : 10.901 88.557 9912 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.45 % Favored : 93.07 % Rotamer: Outliers : 0.14 % Allowed : 0.65 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.62 % 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: -0.76 (0.14), residues: 3147 helix: 0.52 (0.19), residues: 624 sheet: 0.64 (0.21), residues: 560 loop : -1.26 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP A 866 HIS 0.005 0.001 HIS C 499 PHE 0.025 0.003 PHE B 122 TYR 0.035 0.004 TYR C 187 ARG 0.003 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 537 time to evaluate : 2.678 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 79 PHE cc_start: 0.4536 (m-80) cc_final: 0.2844 (m-80) REVERT: A 164 MET cc_start: 0.5980 (tpt) cc_final: 0.4901 (mmm) REVERT: A 176 LEU cc_start: 0.7641 (pp) cc_final: 0.7426 (pp) REVERT: A 544 GLN cc_start: 0.6350 (mm-40) cc_final: 0.5957 (mm110) REVERT: A 572 PHE cc_start: 0.7997 (p90) cc_final: 0.7759 (p90) REVERT: A 634 GLU cc_start: 0.8209 (tt0) cc_final: 0.7983 (tt0) REVERT: A 717 ASP cc_start: 0.7926 (t0) cc_final: 0.7720 (t0) REVERT: A 848 GLU cc_start: 0.8186 (mp0) cc_final: 0.7923 (mm-30) REVERT: B 79 PHE cc_start: 0.4919 (m-80) cc_final: 0.4374 (m-80) REVERT: B 179 PHE cc_start: 0.8205 (m-80) cc_final: 0.7952 (m-10) REVERT: B 187 TYR cc_start: 0.7370 (m-80) cc_final: 0.7068 (m-80) REVERT: B 249 TYR cc_start: 0.7436 (m-80) cc_final: 0.6971 (m-80) REVERT: B 517 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7061 (tptt) REVERT: B 552 THR cc_start: 0.7674 (p) cc_final: 0.7236 (m) REVERT: B 1116 THR cc_start: 0.8589 (m) cc_final: 0.8383 (p) REVERT: B 1118 TYR cc_start: 0.7152 (m-80) cc_final: 0.6838 (m-80) REVERT: C 193 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7782 (mmmt) REVERT: C 288 VAL cc_start: 0.8697 (t) cc_final: 0.8280 (t) REVERT: C 293 TYR cc_start: 0.8660 (m-80) cc_final: 0.8063 (m-80) REVERT: C 296 SER cc_start: 0.8309 (t) cc_final: 0.7754 (m) REVERT: C 297 ASN cc_start: 0.8550 (m-40) cc_final: 0.8109 (m-40) REVERT: C 333 TRP cc_start: 0.6253 (p90) cc_final: 0.5763 (p90) REVERT: C 369 ASP cc_start: 0.7792 (m-30) cc_final: 0.7451 (m-30) REVERT: C 432 GLN cc_start: 0.5805 (mt0) cc_final: 0.5401 (mp10) REVERT: C 754 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8612 (mp10) REVERT: C 836 ASN cc_start: 0.6947 (m-40) cc_final: 0.6690 (m110) REVERT: C 947 SER cc_start: 0.8700 (m) cc_final: 0.8475 (p) REVERT: C 985 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8291 (tp40) outliers start: 4 outliers final: 2 residues processed: 541 average time/residue: 0.4028 time to fit residues: 333.4727 Evaluate side-chains 256 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain C residue 1054 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.2980 chunk 238 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.0010 chunk 183 optimal weight: 0.6980 chunk 286 optimal weight: 4.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 635 HIS A 935 ASN A 990 GLN A1038 HIS B 670 GLN B 836 ASN ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 GLN C 205 GLN C 594 ASN C 990 GLN C1081 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25883 Z= 0.206 Angle : 0.694 12.914 35224 Z= 0.373 Chirality : 0.049 0.272 4094 Planarity : 0.004 0.045 4535 Dihedral : 6.040 58.043 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.59 % Favored : 94.22 % Rotamer: Outliers : 1.62 % Allowed : 6.08 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -0.56 (0.15), residues: 3147 helix: 1.80 (0.21), residues: 618 sheet: 0.24 (0.20), residues: 634 loop : -1.41 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 866 HIS 0.012 0.001 HIS B 49 PHE 0.029 0.002 PHE C 380 TYR 0.021 0.002 TYR C 403 ARG 0.013 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 3.023 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 113 VAL cc_start: 0.7272 (p) cc_final: 0.6993 (p) REVERT: A 164 MET cc_start: 0.5910 (tpt) cc_final: 0.5500 (mmm) REVERT: A 176 LEU cc_start: 0.7505 (pp) cc_final: 0.7099 (pp) REVERT: A 178 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7205 (mp0) REVERT: A 181 PHE cc_start: 0.6914 (t80) cc_final: 0.6647 (t80) REVERT: A 371 CYS cc_start: 0.8187 (m) cc_final: 0.7947 (m) REVERT: A 682 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 717 ASP cc_start: 0.7917 (t0) cc_final: 0.7607 (t0) REVERT: B 157 TYR cc_start: 0.7169 (p90) cc_final: 0.6910 (p90) REVERT: B 179 PHE cc_start: 0.8071 (m-80) cc_final: 0.7769 (m-80) REVERT: B 249 TYR cc_start: 0.7140 (m-80) cc_final: 0.6500 (m-80) REVERT: B 512 ASN cc_start: 0.8175 (t0) cc_final: 0.7965 (t0) REVERT: B 537 LYS cc_start: 0.2609 (tmtt) cc_final: 0.2377 (tttm) REVERT: B 836 ASN cc_start: 0.8620 (m110) cc_final: 0.8400 (m110) REVERT: B 849 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7569 (mtm) REVERT: B 1078 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7937 (t0) REVERT: C 193 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7593 (mmmt) REVERT: C 296 SER cc_start: 0.8239 (t) cc_final: 0.7910 (m) REVERT: C 297 ASN cc_start: 0.8510 (m-40) cc_final: 0.8272 (m-40) REVERT: C 333 TRP cc_start: 0.5709 (p90) cc_final: 0.5229 (p90) REVERT: C 369 ASP cc_start: 0.7598 (m-30) cc_final: 0.7315 (m-30) REVERT: C 380 PHE cc_start: 0.6601 (m-80) cc_final: 0.6269 (m-80) REVERT: C 432 GLN cc_start: 0.5593 (mt0) cc_final: 0.5366 (mp10) REVERT: C 947 SER cc_start: 0.8644 (m) cc_final: 0.8363 (p) REVERT: C 985 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8381 (tp40) outliers start: 45 outliers final: 25 residues processed: 333 average time/residue: 0.3717 time to fit residues: 195.7142 Evaluate side-chains 240 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 800 ASP Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1054 ASN Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 286 optimal weight: 8.9990 chunk 309 optimal weight: 0.7980 chunk 255 optimal weight: 7.9990 chunk 284 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 ASN C 929 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25883 Z= 0.198 Angle : 0.629 12.226 35224 Z= 0.335 Chirality : 0.047 0.403 4094 Planarity : 0.004 0.040 4535 Dihedral : 5.808 58.275 4204 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 1.66 % Allowed : 8.17 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3147 helix: 1.85 (0.21), residues: 619 sheet: 0.04 (0.20), residues: 639 loop : -1.39 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 139 HIS 0.008 0.001 HIS C 499 PHE 0.030 0.002 PHE C 380 TYR 0.022 0.001 TYR C 403 ARG 0.011 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 2.902 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 113 VAL cc_start: 0.7212 (p) cc_final: 0.6954 (p) REVERT: A 164 MET cc_start: 0.6090 (tpt) cc_final: 0.5419 (mmm) REVERT: A 176 LEU cc_start: 0.7477 (pp) cc_final: 0.6946 (pp) REVERT: A 178 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7256 (mp0) REVERT: A 181 PHE cc_start: 0.6978 (t80) cc_final: 0.6626 (t80) REVERT: A 369 ASP cc_start: 0.7062 (m-30) cc_final: 0.6689 (t70) REVERT: A 371 CYS cc_start: 0.8077 (m) cc_final: 0.7817 (m) REVERT: A 682 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 740 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7493 (m) REVERT: B 179 PHE cc_start: 0.7990 (m-80) cc_final: 0.7768 (m-80) REVERT: B 249 TYR cc_start: 0.7019 (m-80) cc_final: 0.6325 (m-80) REVERT: B 512 ASN cc_start: 0.8196 (t0) cc_final: 0.7909 (t0) REVERT: B 836 ASN cc_start: 0.8641 (m110) cc_final: 0.8430 (m110) REVERT: B 929 GLN cc_start: 0.8626 (tp40) cc_final: 0.8348 (mm-40) REVERT: C 250 LEU cc_start: 0.7518 (mp) cc_final: 0.7191 (mp) REVERT: C 296 SER cc_start: 0.8367 (t) cc_final: 0.8081 (m) REVERT: C 333 TRP cc_start: 0.5591 (p90) cc_final: 0.5270 (p90) REVERT: C 369 ASP cc_start: 0.7696 (m-30) cc_final: 0.7423 (m-30) REVERT: C 376 TYR cc_start: 0.6237 (m-80) cc_final: 0.5941 (m-80) REVERT: C 380 PHE cc_start: 0.6574 (m-80) cc_final: 0.6260 (m-10) REVERT: C 416 TRP cc_start: 0.5760 (p90) cc_final: 0.5536 (p90) REVERT: C 432 GLN cc_start: 0.5542 (mt0) cc_final: 0.5288 (mp10) REVERT: C 742 GLN cc_start: 0.8742 (mm110) cc_final: 0.8337 (mt0) REVERT: C 947 SER cc_start: 0.8628 (m) cc_final: 0.8351 (p) REVERT: C 985 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8380 (tp40) outliers start: 46 outliers final: 27 residues processed: 268 average time/residue: 0.3490 time to fit residues: 152.5010 Evaluate side-chains 221 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 1126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN B 49 HIS ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 124 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 635 HIS C 894 ASN C 982 GLN C1068 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 25883 Z= 0.366 Angle : 0.710 11.491 35224 Z= 0.373 Chirality : 0.050 0.315 4094 Planarity : 0.004 0.057 4535 Dihedral : 6.429 57.700 4202 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.50 % Favored : 92.41 % Rotamer: Outliers : 2.12 % Allowed : 9.43 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.06 (0.15), residues: 3147 helix: 1.49 (0.21), residues: 621 sheet: -0.37 (0.20), residues: 619 loop : -1.66 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 866 HIS 0.007 0.001 HIS B1044 PHE 0.026 0.002 PHE C 521 TYR 0.029 0.002 TYR B1047 ARG 0.007 0.001 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 3.044 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 164 MET cc_start: 0.5949 (tpt) cc_final: 0.5272 (mmm) REVERT: A 176 LEU cc_start: 0.7474 (pp) cc_final: 0.7168 (pp) REVERT: A 178 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7046 (mp0) REVERT: A 740 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7583 (m) REVERT: B 249 TYR cc_start: 0.6861 (m-80) cc_final: 0.6207 (m-80) REVERT: B 547 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7624 (mmm-85) REVERT: B 836 ASN cc_start: 0.8652 (m110) cc_final: 0.8425 (m110) REVERT: B 929 GLN cc_start: 0.8712 (tp40) cc_final: 0.8385 (mm-40) REVERT: B 963 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8191 (ttm170) REVERT: C 210 LEU cc_start: 0.7788 (mt) cc_final: 0.7559 (mm) REVERT: C 250 LEU cc_start: 0.7444 (mp) cc_final: 0.7087 (mp) REVERT: C 333 TRP cc_start: 0.5498 (p90) cc_final: 0.5150 (p90) REVERT: C 369 ASP cc_start: 0.7944 (m-30) cc_final: 0.7579 (m-30) REVERT: C 380 PHE cc_start: 0.6451 (m-80) cc_final: 0.6214 (m-10) REVERT: C 416 TRP cc_start: 0.5733 (p90) cc_final: 0.5518 (p90) REVERT: C 432 GLN cc_start: 0.5484 (mt0) cc_final: 0.5123 (mp10) REVERT: C 473 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6127 (mt0) REVERT: C 728 GLU cc_start: 0.7980 (mp0) cc_final: 0.7658 (mp0) REVERT: C 742 GLN cc_start: 0.8764 (mm110) cc_final: 0.8436 (mt0) outliers start: 59 outliers final: 39 residues processed: 266 average time/residue: 0.3779 time to fit residues: 164.0258 Evaluate side-chains 225 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 839 ASN B 49 HIS B 205 GLN B 593 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 ASN C 881 GLN C 985 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 25883 Z= 0.597 Angle : 0.827 12.266 35224 Z= 0.430 Chirality : 0.055 0.360 4094 Planarity : 0.005 0.055 4535 Dihedral : 7.276 59.629 4202 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.99 % Favored : 90.91 % Rotamer: Outliers : 2.73 % Allowed : 10.47 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.79 (0.14), residues: 3147 helix: 0.84 (0.21), residues: 630 sheet: -0.84 (0.19), residues: 626 loop : -2.14 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 866 HIS 0.012 0.002 HIS C 499 PHE 0.026 0.003 PHE A1069 TYR 0.035 0.003 TYR B1047 ARG 0.013 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 212 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.5972 (tpt) cc_final: 0.5343 (mmm) REVERT: A 178 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7273 (mp0) REVERT: B 157 TYR cc_start: 0.7293 (p90) cc_final: 0.7085 (p90) REVERT: B 249 TYR cc_start: 0.6800 (m-80) cc_final: 0.6142 (m-80) REVERT: B 547 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7644 (mmm-85) REVERT: B 836 ASN cc_start: 0.8665 (m110) cc_final: 0.8429 (m110) REVERT: B 963 ARG cc_start: 0.8483 (mtp180) cc_final: 0.8181 (ttm170) REVERT: C 333 TRP cc_start: 0.5922 (p90) cc_final: 0.5550 (p90) REVERT: C 369 ASP cc_start: 0.8077 (m-30) cc_final: 0.7745 (m-30) REVERT: C 380 PHE cc_start: 0.6354 (m-80) cc_final: 0.6040 (m-10) REVERT: C 432 GLN cc_start: 0.5408 (mt0) cc_final: 0.5179 (mp10) REVERT: C 473 GLN cc_start: 0.6439 (mm-40) cc_final: 0.6153 (tm-30) REVERT: C 512 ASN cc_start: 0.8027 (m-40) cc_final: 0.7770 (t0) REVERT: C 742 GLN cc_start: 0.8875 (mm110) cc_final: 0.8506 (mt0) outliers start: 76 outliers final: 51 residues processed: 274 average time/residue: 0.3430 time to fit residues: 152.9765 Evaluate side-chains 235 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1061 ILE Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 894 ASN Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1085 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 141 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 160 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 839 ASN B 226 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS C 594 ASN C 754 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25883 Z= 0.199 Angle : 0.644 11.664 35224 Z= 0.338 Chirality : 0.047 0.316 4094 Planarity : 0.004 0.041 4535 Dihedral : 6.680 59.575 4202 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 1.94 % Allowed : 11.80 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.40 (0.15), residues: 3147 helix: 1.50 (0.21), residues: 630 sheet: -0.72 (0.20), residues: 616 loop : -1.96 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 416 HIS 0.010 0.001 HIS A 232 PHE 0.029 0.002 PHE C 380 TYR 0.019 0.001 TYR C 431 ARG 0.005 0.000 ARG C 975 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7259 (mp0) REVERT: A 725 ASP cc_start: 0.8284 (p0) cc_final: 0.8075 (p0) REVERT: A 740 CYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7584 (m) REVERT: B 249 TYR cc_start: 0.6564 (m-80) cc_final: 0.5983 (m-80) REVERT: B 963 ARG cc_start: 0.8539 (mtp180) cc_final: 0.8297 (ttm170) REVERT: C 473 GLN cc_start: 0.6550 (mm-40) cc_final: 0.5773 (mt0) REVERT: C 728 GLU cc_start: 0.7650 (mp0) cc_final: 0.7376 (mp0) REVERT: C 742 GLN cc_start: 0.8683 (mm110) cc_final: 0.8322 (mt0) outliers start: 54 outliers final: 42 residues processed: 246 average time/residue: 0.3426 time to fit residues: 138.8714 Evaluate side-chains 226 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 256 optimal weight: 0.3980 chunk 170 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 190 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25883 Z= 0.205 Angle : 0.628 12.578 35224 Z= 0.326 Chirality : 0.046 0.321 4094 Planarity : 0.004 0.043 4535 Dihedral : 6.380 58.343 4202 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.24 % Favored : 92.66 % Rotamer: Outliers : 2.20 % Allowed : 12.09 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.30 (0.15), residues: 3147 helix: 1.75 (0.21), residues: 624 sheet: -0.77 (0.19), residues: 629 loop : -1.90 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 416 HIS 0.008 0.001 HIS A 232 PHE 0.021 0.001 PHE A 495 TYR 0.020 0.001 TYR B1047 ARG 0.007 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7353 (mp0) REVERT: A 725 ASP cc_start: 0.8323 (p0) cc_final: 0.8094 (p0) REVERT: A 740 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7516 (m) REVERT: B 249 TYR cc_start: 0.6690 (m-80) cc_final: 0.6343 (m-80) REVERT: B 547 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: B 963 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8213 (ttm170) REVERT: C 249 TYR cc_start: 0.6340 (m-10) cc_final: 0.5901 (m-80) REVERT: C 473 GLN cc_start: 0.6565 (mm-40) cc_final: 0.5732 (mt0) REVERT: C 728 GLU cc_start: 0.7555 (mp0) cc_final: 0.7218 (mp0) REVERT: C 742 GLN cc_start: 0.8654 (mm110) cc_final: 0.8321 (mt0) REVERT: C 970 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8103 (tt0) outliers start: 61 outliers final: 43 residues processed: 239 average time/residue: 0.3378 time to fit residues: 134.9578 Evaluate side-chains 226 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 GLN ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 25883 Z= 0.356 Angle : 0.681 11.549 35224 Z= 0.353 Chirality : 0.049 0.326 4094 Planarity : 0.004 0.045 4535 Dihedral : 6.661 59.948 4202 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.87 % Favored : 91.04 % Rotamer: Outliers : 2.30 % Allowed : 12.23 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.51 (0.15), residues: 3147 helix: 1.46 (0.21), residues: 630 sheet: -0.91 (0.19), residues: 637 loop : -2.02 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 416 HIS 0.005 0.001 HIS B1044 PHE 0.021 0.002 PHE A 495 TYR 0.027 0.002 TYR B1047 ARG 0.005 0.001 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 187 time to evaluate : 2.702 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 178 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7434 (mp0) REVERT: A 725 ASP cc_start: 0.8430 (p0) cc_final: 0.8199 (p0) REVERT: B 547 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7532 (mmm-85) REVERT: B 963 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8083 (ttm170) REVERT: C 41 LYS cc_start: 0.7448 (mmtm) cc_final: 0.6712 (pttt) REVERT: C 473 GLN cc_start: 0.6497 (mm-40) cc_final: 0.5766 (mt0) REVERT: C 728 GLU cc_start: 0.7633 (mp0) cc_final: 0.7308 (mp0) REVERT: C 742 GLN cc_start: 0.8774 (mm110) cc_final: 0.8386 (mt0) outliers start: 64 outliers final: 43 residues processed: 242 average time/residue: 0.3617 time to fit residues: 145.9085 Evaluate side-chains 226 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.5980 chunk 290 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 281 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25883 Z= 0.183 Angle : 0.618 11.759 35224 Z= 0.322 Chirality : 0.046 0.323 4094 Planarity : 0.004 0.039 4535 Dihedral : 6.258 56.869 4202 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.37 % Favored : 92.53 % Rotamer: Outliers : 1.76 % Allowed : 12.85 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.33 (0.15), residues: 3147 helix: 1.77 (0.22), residues: 624 sheet: -0.84 (0.20), residues: 627 loop : -1.93 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 416 HIS 0.006 0.001 HIS A 232 PHE 0.021 0.001 PHE A 495 TYR 0.019 0.001 TYR B 157 ARG 0.006 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 199 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7372 (mp0) REVERT: A 725 ASP cc_start: 0.8365 (p0) cc_final: 0.8140 (p0) REVERT: B 963 ARG cc_start: 0.8506 (mtp180) cc_final: 0.8139 (ttm170) REVERT: C 249 TYR cc_start: 0.6404 (m-10) cc_final: 0.6064 (m-80) REVERT: C 473 GLN cc_start: 0.6620 (mm-40) cc_final: 0.5833 (mt0) REVERT: C 728 GLU cc_start: 0.7529 (mp0) cc_final: 0.7194 (mp0) REVERT: C 742 GLN cc_start: 0.8639 (mm110) cc_final: 0.8282 (mt0) REVERT: C 970 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8106 (tt0) outliers start: 49 outliers final: 43 residues processed: 237 average time/residue: 0.3471 time to fit residues: 137.1377 Evaluate side-chains 232 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.9980 chunk 299 optimal weight: 0.0670 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 207 optimal weight: 0.0870 chunk 313 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 ASN B 49 HIS ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25883 Z= 0.185 Angle : 0.616 12.360 35224 Z= 0.317 Chirality : 0.046 0.323 4094 Planarity : 0.004 0.040 4535 Dihedral : 6.074 57.198 4202 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 1.66 % Allowed : 13.17 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.57 % 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: -1.25 (0.15), residues: 3147 helix: 1.82 (0.22), residues: 630 sheet: -0.83 (0.20), residues: 634 loop : -1.87 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 416 HIS 0.006 0.001 HIS A 232 PHE 0.023 0.001 PHE A 179 TYR 0.021 0.001 TYR B 897 ARG 0.006 0.000 ARG B 547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7375 (mp0) REVERT: A 725 ASP cc_start: 0.8372 (p0) cc_final: 0.8142 (p0) REVERT: B 547 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: B 963 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8133 (ttm170) REVERT: C 473 GLN cc_start: 0.6678 (mm-40) cc_final: 0.5903 (mt0) REVERT: C 728 GLU cc_start: 0.7471 (mp0) cc_final: 0.7130 (mp0) REVERT: C 742 GLN cc_start: 0.8623 (mm110) cc_final: 0.8225 (mt0) REVERT: C 970 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8101 (tt0) outliers start: 46 outliers final: 44 residues processed: 225 average time/residue: 0.3344 time to fit residues: 124.6461 Evaluate side-chains 228 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 CYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1038 HIS Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1099 ASN Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 834 LYS Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 1052 GLU Chi-restraints excluded: chain B residue 1103 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 91 TRP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 495 PHE Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 653 SER Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1084 VAL Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 230 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 250 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 451 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.173152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123116 restraints weight = 41815.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122713 restraints weight = 42542.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116294 restraints weight = 26944.513| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25883 Z= 0.303 Angle : 0.657 11.571 35224 Z= 0.339 Chirality : 0.048 0.326 4094 Planarity : 0.004 0.043 4535 Dihedral : 6.319 59.074 4202 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.58 % Favored : 91.29 % Rotamer: Outliers : 1.69 % Allowed : 13.35 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 3147 helix: 1.67 (0.21), residues: 624 sheet: -0.91 (0.20), residues: 638 loop : -1.95 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 866 HIS 0.005 0.001 HIS B1044 PHE 0.039 0.002 PHE C 521 TYR 0.028 0.002 TYR A 433 ARG 0.005 0.000 ARG C 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.21 seconds wall clock time: 100 minutes 8.91 seconds (6008.91 seconds total)