Starting phenix.real_space_refine on Thu Jul 25 20:36:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbf_38216/07_2024/8xbf_38216.cif" } resolution = 3.6 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= 0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 19155 2.51 5 N 5026 2.21 5 O 5782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30099 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "B" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "C" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "E" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 871 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 16.25, per 1000 atoms: 0.54 Number of scatterers: 30099 At special positions: 0 Unit cell: (149.04, 159.84, 209.52, 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 136 16.00 O 5782 8.00 N 5026 7.00 C 19155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 98 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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 A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C1134 " Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 5.3 seconds 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7124 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 63 sheets defined 21.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.513A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.250A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 857 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.026A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.533A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.891A pdb=" N SER A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.110A pdb=" N VAL B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.817A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.742A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.736A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.577A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.201A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 3.834A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.848A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.535A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.648A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.953A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.533A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.449A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.648A pdb=" N SER C1147 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.620A pdb=" N ASN D 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.554A pdb=" N THR D 93 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.889A pdb=" N THR F 93 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.382A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.499A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.529A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 197 removed outlier: 5.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.567A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.979A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.575A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 656 removed outlier: 4.672A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.401A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.608A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 22 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.422A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AC7, first strand: chain 'B' and resid 203 through 205 removed outlier: 7.906A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.154A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.550A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.579A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.106A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 7.254A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 22 through 30 removed outlier: 3.781A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.648A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.182A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.777A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.484A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.753A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.650A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.635A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.712A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AF9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.140A pdb=" N GLY D 13 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 36 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D 37 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.140A pdb=" N GLY D 13 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 108 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.083A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.083A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 97 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AG6, first strand: chain 'F' and resid 14 through 15 removed outlier: 3.608A pdb=" N TYR F 36 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 14 through 15 removed outlier: 6.387A pdb=" N ARG F 100 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 5 through 7 removed outlier: 4.230A pdb=" N ASP G 17 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL G 19 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER G 76 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE G 21 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR G 74 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYS G 23 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR G 72 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.460A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.48 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9699 1.35 - 1.47: 7676 1.47 - 1.59: 13263 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 30812 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA TRP G 32 " pdb=" C TRP G 32 " ideal model delta sigma weight residual 1.524 1.567 -0.043 1.47e-02 4.63e+03 8.64e+00 bond pdb=" C LEU B 223 " pdb=" N GLU B 224 " ideal model delta sigma weight residual 1.333 1.403 -0.071 2.74e-02 1.33e+03 6.65e+00 ... (remaining 30807 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.33: 875 106.33 - 113.25: 16615 113.25 - 120.16: 10358 120.16 - 127.07: 13775 127.07 - 133.99: 310 Bond angle restraints: 41933 Sorted by residual: angle pdb=" C TYR C1067 " pdb=" N VAL C1068 " pdb=" CA VAL C1068 " ideal model delta sigma weight residual 122.85 119.61 3.24 8.70e-01 1.32e+00 1.39e+01 angle pdb=" CA TRP G 32 " pdb=" C TRP G 32 " pdb=" N LEU G 33 " ideal model delta sigma weight residual 117.40 122.16 -4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C TYR G 94 " pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta sigma weight residual 120.82 125.79 -4.97 1.50e+00 4.44e-01 1.10e+01 angle pdb=" CA GLY A 700 " pdb=" C GLY A 700 " pdb=" N ALA A 701 " ideal model delta sigma weight residual 114.23 116.90 -2.67 8.80e-01 1.29e+00 9.21e+00 angle pdb=" CA TRP G 32 " pdb=" C TRP G 32 " pdb=" O TRP G 32 " ideal model delta sigma weight residual 120.32 117.35 2.97 1.02e+00 9.61e-01 8.49e+00 ... (remaining 41928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 17738 24.31 - 48.62: 697 48.62 - 72.93: 128 72.93 - 97.24: 24 97.24 - 121.55: 7 Dihedral angle restraints: 18594 sinusoidal: 7469 harmonic: 11125 Sorted by residual: dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA VAL B 267 " pdb=" C VAL B 267 " pdb=" N GLY B 268 " pdb=" CA GLY B 268 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA TYR G 94 " pdb=" C TYR G 94 " pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 18591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4542 0.100 - 0.200: 218 0.200 - 0.300: 0 0.300 - 0.400: 0 0.400 - 0.500: 2 Chirality restraints: 4762 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4759 not shown) Planarity restraints: 5429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO B 561 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 986 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 330 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.025 5.00e-02 4.00e+02 ... (remaining 5426 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 610 2.63 - 3.19: 28497 3.19 - 3.76: 48758 3.76 - 4.33: 67364 4.33 - 4.90: 107938 Nonbonded interactions: 253167 Sorted by model distance: nonbonded pdb=" O GLY A 496 " pdb=" OH TYR A 501 " model vdw 2.057 2.440 nonbonded pdb=" OG SER C 659 " pdb=" O THR C 696 " model vdw 2.096 2.440 nonbonded pdb=" OG SER G 63 " pdb=" O THR G 74 " model vdw 2.118 2.440 nonbonded pdb=" OG SER A 659 " pdb=" O THR A 696 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR B 22 " pdb=" O HIS B 66 " model vdw 2.138 2.440 ... (remaining 253162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 79.690 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30812 Z= 0.245 Angle : 0.629 10.653 41933 Z= 0.344 Chirality : 0.045 0.500 4762 Planarity : 0.004 0.068 5411 Dihedral : 13.647 121.547 11332 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.28 % Allowed : 10.37 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.13), residues: 3819 helix: 0.72 (0.19), residues: 753 sheet: -1.24 (0.19), residues: 677 loop : -1.39 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 32 HIS 0.004 0.001 HIS G 90 PHE 0.018 0.001 PHE A 565 TYR 0.018 0.001 TYR B 170 ARG 0.004 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 90 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: A 398 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6456 (p0) REVERT: A 465 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.3267 (tt0) REVERT: A 740 MET cc_start: 0.8386 (tpt) cc_final: 0.8046 (tpt) REVERT: A 1119 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 177 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4629 (mmp) REVERT: B 310 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6730 (ptmm) REVERT: B 508 TYR cc_start: 0.7951 (m-10) cc_final: 0.7685 (m-10) REVERT: B 573 THR cc_start: 0.0556 (OUTLIER) cc_final: -0.1868 (t) REVERT: B 727 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8796 (mm) REVERT: B 894 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 196 ASN cc_start: 0.4667 (OUTLIER) cc_final: 0.3945 (p0) REVERT: C 258 TRP cc_start: 0.4641 (OUTLIER) cc_final: 0.1359 (p90) REVERT: C 900 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7454 (mtm) REVERT: C 1073 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6723 (mmmt) REVERT: D 37 MET cc_start: -0.3044 (OUTLIER) cc_final: -0.3275 (mtp) REVERT: E 77 SER cc_start: 0.5699 (OUTLIER) cc_final: 0.5096 (p) REVERT: F 107 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7228 (p0) outliers start: 175 outliers final: 65 residues processed: 253 average time/residue: 0.3838 time to fit residues: 161.4392 Evaluate side-chains 148 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 67 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 220 optimal weight: 0.7980 chunk 343 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 354 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 450 ASN A 544 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN B 914 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1088 HIS C 370 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 953 ASN C1054 GLN D 42 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 42 GLN G 6 GLN G 37 GLN G 38 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 30812 Z= 0.387 Angle : 0.692 13.722 41933 Z= 0.362 Chirality : 0.047 0.461 4762 Planarity : 0.005 0.061 5411 Dihedral : 9.877 109.902 4679 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.98 % Favored : 90.99 % Rotamer: Outliers : 5.22 % Allowed : 12.69 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3819 helix: 0.70 (0.19), residues: 750 sheet: -1.51 (0.18), residues: 713 loop : -1.49 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 32 HIS 0.006 0.001 HIS A1058 PHE 0.040 0.002 PHE A 559 TYR 0.035 0.002 TYR B 91 ARG 0.006 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 76 time to evaluate : 4.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: A 398 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6369 (p0) REVERT: A 465 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.3698 (tt0) REVERT: A 740 MET cc_start: 0.8437 (tpt) cc_final: 0.8174 (tpt) REVERT: A 855 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: A 1119 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7869 (p0) REVERT: B 172 SER cc_start: 0.1580 (OUTLIER) cc_final: -0.1067 (p) REVERT: B 204 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.4688 (m-80) REVERT: B 310 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6737 (ptmm) REVERT: B 508 TYR cc_start: 0.8062 (m-10) cc_final: 0.7806 (m-10) REVERT: B 573 THR cc_start: 0.1120 (OUTLIER) cc_final: -0.0925 (t) REVERT: B 661 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: B 693 ILE cc_start: 0.4775 (OUTLIER) cc_final: 0.4503 (pp) REVERT: B 727 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8885 (mm) REVERT: B 894 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 196 ASN cc_start: 0.4945 (OUTLIER) cc_final: 0.4188 (p0) REVERT: C 258 TRP cc_start: 0.4449 (OUTLIER) cc_final: 0.1256 (p90) REVERT: C 284 THR cc_start: 0.6930 (OUTLIER) cc_final: 0.6676 (m) REVERT: C 693 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6161 (pp) REVERT: C 1073 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6788 (mmmt) REVERT: D 82 PHE cc_start: 0.7438 (m-80) cc_final: 0.7199 (m-80) outliers start: 173 outliers final: 84 residues processed: 238 average time/residue: 0.4010 time to fit residues: 160.9668 Evaluate side-chains 169 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 67 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 341 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 30812 Z= 0.276 Angle : 0.626 10.119 41933 Z= 0.323 Chirality : 0.046 0.433 4762 Planarity : 0.004 0.059 5411 Dihedral : 9.358 107.668 4649 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.88 % Allowed : 14.02 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3819 helix: 0.81 (0.19), residues: 759 sheet: -1.60 (0.18), residues: 732 loop : -1.48 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 32 HIS 0.004 0.001 HIS A1058 PHE 0.026 0.002 PHE A 559 TYR 0.028 0.002 TYR B 170 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 71 time to evaluate : 3.510 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 365 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: A 398 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6301 (p0) REVERT: A 465 GLU cc_start: 0.4564 (OUTLIER) cc_final: 0.3887 (tt0) REVERT: A 498 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.5327 (mtm180) REVERT: A 740 MET cc_start: 0.8363 (tpt) cc_final: 0.8136 (tpt) REVERT: A 855 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: A 1119 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7779 (p0) REVERT: B 172 SER cc_start: 0.1468 (OUTLIER) cc_final: -0.0948 (p) REVERT: B 204 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: B 310 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6889 (ptmm) REVERT: B 486 VAL cc_start: 0.3819 (OUTLIER) cc_final: 0.3581 (t) REVERT: B 573 THR cc_start: 0.0710 (OUTLIER) cc_final: -0.1424 (t) REVERT: B 693 ILE cc_start: 0.4817 (OUTLIER) cc_final: 0.4571 (pp) REVERT: B 727 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8846 (mm) REVERT: C 167 THR cc_start: 0.0210 (OUTLIER) cc_final: -0.1354 (t) REVERT: C 196 ASN cc_start: 0.4919 (OUTLIER) cc_final: 0.3863 (p0) REVERT: C 258 TRP cc_start: 0.4386 (OUTLIER) cc_final: 0.1346 (p90) REVERT: C 284 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6454 (m) REVERT: C 559 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5278 (t80) REVERT: C 693 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6078 (pp) REVERT: C 1073 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6691 (mmmt) REVERT: G 32 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.2301 (p-90) outliers start: 162 outliers final: 95 residues processed: 226 average time/residue: 0.3868 time to fit residues: 145.1292 Evaluate side-chains 184 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 68 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 20.0000 chunk 258 optimal weight: 50.0000 chunk 178 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 345 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 544 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 30812 Z= 0.407 Angle : 0.720 16.315 41933 Z= 0.376 Chirality : 0.048 0.405 4762 Planarity : 0.005 0.063 5411 Dihedral : 9.394 107.702 4643 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.90 % Favored : 90.08 % Rotamer: Outliers : 5.49 % Allowed : 14.95 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3819 helix: 0.78 (0.19), residues: 717 sheet: -1.82 (0.17), residues: 740 loop : -1.61 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 32 HIS 0.013 0.001 HIS B 505 PHE 0.032 0.002 PHE A 559 TYR 0.034 0.002 TYR B 91 ARG 0.006 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 73 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.7122 (m110) REVERT: A 365 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: A 398 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6348 (p0) REVERT: A 465 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4285 (tt0) REVERT: A 498 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5022 (mtm180) REVERT: A 740 MET cc_start: 0.8366 (tpt) cc_final: 0.8080 (tpt) REVERT: A 855 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: A 1119 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7902 (p0) REVERT: B 172 SER cc_start: 0.2115 (OUTLIER) cc_final: -0.0445 (p) REVERT: B 204 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.5219 (m-10) REVERT: B 277 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6052 (mm) REVERT: B 512 VAL cc_start: -0.4412 (OUTLIER) cc_final: -0.4879 (m) REVERT: B 573 THR cc_start: 0.1393 (OUTLIER) cc_final: -0.0526 (t) REVERT: B 693 ILE cc_start: 0.4862 (OUTLIER) cc_final: 0.4613 (pp) REVERT: B 727 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8909 (mm) REVERT: C 167 THR cc_start: -0.0086 (OUTLIER) cc_final: -0.1747 (t) REVERT: C 196 ASN cc_start: 0.5286 (OUTLIER) cc_final: 0.4287 (p0) REVERT: C 242 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7292 (tt) REVERT: C 258 TRP cc_start: 0.4512 (OUTLIER) cc_final: 0.1491 (p90) REVERT: C 559 PHE cc_start: 0.5980 (OUTLIER) cc_final: 0.5476 (t80) REVERT: C 693 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6124 (pp) REVERT: C 1073 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6747 (mmmt) REVERT: E 4 MET cc_start: 0.5259 (pmm) cc_final: 0.4638 (pmm) REVERT: E 71 PHE cc_start: 0.4707 (OUTLIER) cc_final: 0.4390 (m-80) REVERT: G 32 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.2048 (p-90) REVERT: G 70 GLU cc_start: 0.4195 (OUTLIER) cc_final: 0.3730 (pp20) outliers start: 182 outliers final: 117 residues processed: 247 average time/residue: 0.3769 time to fit residues: 156.9817 Evaluate side-chains 212 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 71 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 5 optimal weight: 50.0000 chunk 272 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 30812 Z= 0.306 Angle : 0.649 13.587 41933 Z= 0.335 Chirality : 0.046 0.399 4762 Planarity : 0.005 0.058 5411 Dihedral : 9.156 104.236 4641 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.06 % Allowed : 16.10 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3819 helix: 0.84 (0.19), residues: 726 sheet: -1.83 (0.17), residues: 747 loop : -1.57 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 32 HIS 0.005 0.001 HIS B 505 PHE 0.031 0.002 PHE A 347 TYR 0.028 0.002 TYR B 170 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 72 time to evaluate : 3.263 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 110 LEU cc_start: -0.0787 (OUTLIER) cc_final: -0.1096 (tp) REVERT: A 282 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7174 (m110) REVERT: A 365 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: A 415 THR cc_start: 0.3795 (OUTLIER) cc_final: 0.3415 (p) REVERT: A 465 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4379 (tt0) REVERT: A 498 ARG cc_start: 0.5541 (OUTLIER) cc_final: 0.4987 (mtm180) REVERT: A 740 MET cc_start: 0.8301 (tpt) cc_final: 0.8061 (tpt) REVERT: A 855 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: A 1119 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.7877 (p0) REVERT: B 133 PHE cc_start: 0.1367 (OUTLIER) cc_final: 0.0856 (t80) REVERT: B 172 SER cc_start: 0.1393 (OUTLIER) cc_final: -0.1126 (p) REVERT: B 204 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.4943 (m-80) REVERT: B 277 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6075 (mm) REVERT: B 418 ILE cc_start: -0.2798 (OUTLIER) cc_final: -0.3077 (mm) REVERT: B 498 ARG cc_start: 0.3492 (OUTLIER) cc_final: 0.2871 (mtt180) REVERT: B 573 THR cc_start: 0.0735 (OUTLIER) cc_final: -0.1464 (t) REVERT: B 693 ILE cc_start: 0.4821 (OUTLIER) cc_final: 0.4582 (pp) REVERT: B 727 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8943 (mm) REVERT: C 167 THR cc_start: 0.0179 (OUTLIER) cc_final: -0.1504 (t) REVERT: C 196 ASN cc_start: 0.5201 (OUTLIER) cc_final: 0.4284 (p0) REVERT: C 218 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6575 (mt0) REVERT: C 242 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7260 (tt) REVERT: C 258 TRP cc_start: 0.4438 (OUTLIER) cc_final: 0.1381 (p90) REVERT: C 559 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5462 (t80) REVERT: C 1073 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6447 (mmmt) REVERT: E 4 MET cc_start: 0.4942 (pmm) cc_final: 0.4387 (pmm) REVERT: G 32 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.2270 (p-90) outliers start: 168 outliers final: 113 residues processed: 233 average time/residue: 0.3927 time to fit residues: 151.8171 Evaluate side-chains 208 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 70 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 4.9990 chunk 329 optimal weight: 0.0060 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30812 Z= 0.203 Angle : 0.594 11.340 41933 Z= 0.303 Chirality : 0.045 0.391 4762 Planarity : 0.005 0.068 5411 Dihedral : 8.812 99.514 4639 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.34 % Allowed : 16.94 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3819 helix: 1.11 (0.19), residues: 726 sheet: -1.71 (0.17), residues: 782 loop : -1.47 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.005 0.001 HIS B1048 PHE 0.016 0.001 PHE A 559 TYR 0.018 0.001 TYR B 170 ARG 0.006 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 73 time to evaluate : 3.157 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 110 LEU cc_start: -0.1025 (OUTLIER) cc_final: -0.1332 (tp) REVERT: A 282 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7136 (m110) REVERT: A 365 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: A 489 TYR cc_start: 0.1418 (OUTLIER) cc_final: 0.0856 (t80) REVERT: A 498 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5207 (mtm180) REVERT: A 855 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6995 (m-10) REVERT: A 1119 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8046 (p0) REVERT: B 133 PHE cc_start: 0.1205 (OUTLIER) cc_final: 0.0743 (t80) REVERT: B 204 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.4507 (m-80) REVERT: B 418 ILE cc_start: -0.2737 (OUTLIER) cc_final: -0.3044 (mm) REVERT: B 512 VAL cc_start: -0.3847 (OUTLIER) cc_final: -0.4229 (m) REVERT: B 573 THR cc_start: 0.0124 (OUTLIER) cc_final: -0.1769 (t) REVERT: C 154 GLU cc_start: 0.3742 (OUTLIER) cc_final: 0.3308 (tp30) REVERT: C 196 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.4388 (p0) REVERT: C 218 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6480 (mt0) REVERT: C 242 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7136 (tt) REVERT: C 258 TRP cc_start: 0.4458 (OUTLIER) cc_final: 0.1396 (p90) REVERT: C 559 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.5336 (t80) REVERT: C 693 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6033 (pp) REVERT: E 4 MET cc_start: 0.4537 (pmm) cc_final: 0.4081 (pmm) REVERT: G 32 TRP cc_start: 0.7564 (OUTLIER) cc_final: 0.2082 (p-90) REVERT: G 70 GLU cc_start: 0.4538 (OUTLIER) cc_final: 0.3904 (pp20) outliers start: 144 outliers final: 94 residues processed: 209 average time/residue: 0.3977 time to fit residues: 137.8754 Evaluate side-chains 184 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 69 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 267 optimal weight: 40.0000 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 30812 Z= 0.433 Angle : 0.722 16.895 41933 Z= 0.378 Chirality : 0.048 0.380 4762 Planarity : 0.005 0.059 5411 Dihedral : 8.979 102.466 4614 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.53 % Favored : 90.44 % Rotamer: Outliers : 5.22 % Allowed : 16.70 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3819 helix: 0.84 (0.19), residues: 720 sheet: -1.80 (0.17), residues: 787 loop : -1.58 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C1102 HIS 0.007 0.001 HIS B 505 PHE 0.026 0.002 PHE B 168 TYR 0.035 0.002 TYR B 170 ARG 0.011 0.001 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 70 time to evaluate : 3.351 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 110 LEU cc_start: -0.0850 (OUTLIER) cc_final: -0.1488 (tt) REVERT: A 282 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.7108 (m110) REVERT: A 365 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: A 415 THR cc_start: 0.3582 (OUTLIER) cc_final: 0.3212 (p) REVERT: A 489 TYR cc_start: 0.1283 (OUTLIER) cc_final: 0.0674 (t80) REVERT: A 498 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5064 (mtm180) REVERT: A 693 ILE cc_start: 0.4419 (OUTLIER) cc_final: 0.4190 (pp) REVERT: A 740 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (tpt) REVERT: A 855 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7041 (m-10) REVERT: A 1119 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 133 PHE cc_start: 0.1506 (OUTLIER) cc_final: 0.0878 (t80) REVERT: B 172 SER cc_start: 0.1889 (OUTLIER) cc_final: -0.0743 (p) REVERT: B 204 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: B 277 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6240 (mm) REVERT: B 512 VAL cc_start: -0.3100 (OUTLIER) cc_final: -0.3506 (m) REVERT: B 573 THR cc_start: 0.1449 (OUTLIER) cc_final: -0.0709 (t) REVERT: C 154 GLU cc_start: 0.3962 (OUTLIER) cc_final: 0.3533 (tp30) REVERT: C 167 THR cc_start: -0.0014 (OUTLIER) cc_final: -0.1742 (t) REVERT: C 196 ASN cc_start: 0.5631 (OUTLIER) cc_final: 0.5154 (p0) REVERT: C 218 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: C 242 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7216 (tt) REVERT: C 258 TRP cc_start: 0.4767 (OUTLIER) cc_final: 0.2037 (p90) REVERT: C 559 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5627 (t80) REVERT: E 4 MET cc_start: 0.5118 (pmm) cc_final: 0.4371 (pmm) REVERT: F 100 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6627 (mmp-170) REVERT: G 32 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.1908 (p-90) outliers start: 173 outliers final: 116 residues processed: 234 average time/residue: 0.3890 time to fit residues: 151.5326 Evaluate side-chains 208 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 67 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30812 Z= 0.227 Angle : 0.619 11.843 41933 Z= 0.316 Chirality : 0.045 0.375 4762 Planarity : 0.004 0.058 5411 Dihedral : 8.612 99.492 4614 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.28 % Allowed : 17.49 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3819 helix: 1.05 (0.19), residues: 726 sheet: -1.74 (0.17), residues: 799 loop : -1.54 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.001 PHE C 43 TYR 0.018 0.001 TYR B 170 ARG 0.009 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 68 time to evaluate : 3.417 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 110 LEU cc_start: -0.0890 (OUTLIER) cc_final: -0.1224 (tp) REVERT: A 282 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7160 (m110) REVERT: A 365 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: A 415 THR cc_start: 0.3851 (OUTLIER) cc_final: 0.3467 (p) REVERT: A 489 TYR cc_start: 0.0758 (OUTLIER) cc_final: 0.0164 (t80) REVERT: A 498 ARG cc_start: 0.5525 (OUTLIER) cc_final: 0.5045 (mtm180) REVERT: A 692 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7507 (tp) REVERT: A 740 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 855 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: A 902 MET cc_start: 0.7804 (tpt) cc_final: 0.7541 (mmm) REVERT: A 1119 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8154 (p0) REVERT: B 133 PHE cc_start: 0.1569 (OUTLIER) cc_final: 0.0887 (t80) REVERT: B 153 MET cc_start: 0.5505 (tpt) cc_final: 0.4879 (tpt) REVERT: B 172 SER cc_start: 0.1068 (OUTLIER) cc_final: -0.1235 (p) REVERT: B 204 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.4667 (m-80) REVERT: B 512 VAL cc_start: -0.3017 (OUTLIER) cc_final: -0.3381 (m) REVERT: B 573 THR cc_start: 0.0354 (OUTLIER) cc_final: -0.1815 (t) REVERT: B 900 MET cc_start: 0.8516 (mmm) cc_final: 0.8207 (mmm) REVERT: B 1050 MET cc_start: 0.8248 (ppp) cc_final: 0.8014 (ptm) REVERT: C 154 GLU cc_start: 0.4008 (OUTLIER) cc_final: 0.3662 (tp30) REVERT: C 167 THR cc_start: -0.0107 (OUTLIER) cc_final: -0.1898 (t) REVERT: C 196 ASN cc_start: 0.5181 (OUTLIER) cc_final: 0.4841 (p0) REVERT: C 218 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6833 (mt0) REVERT: C 242 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6998 (mp) REVERT: C 258 TRP cc_start: 0.4815 (OUTLIER) cc_final: 0.3148 (p90) REVERT: C 559 PHE cc_start: 0.5975 (OUTLIER) cc_final: 0.5438 (t80) REVERT: E 4 MET cc_start: 0.5187 (pmm) cc_final: 0.4706 (pmm) REVERT: F 100 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6002 (mmp-170) REVERT: G 32 TRP cc_start: 0.7531 (OUTLIER) cc_final: 0.1466 (p-90) REVERT: G 70 GLU cc_start: 0.4504 (OUTLIER) cc_final: 0.3863 (pp20) REVERT: G 90 HIS cc_start: 0.4431 (OUTLIER) cc_final: 0.4196 (m90) outliers start: 142 outliers final: 101 residues processed: 201 average time/residue: 0.4059 time to fit residues: 136.8878 Evaluate side-chains 193 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 66 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 90 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 348 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 266 optimal weight: 50.0000 chunk 104 optimal weight: 0.7980 chunk 306 optimal weight: 50.0000 chunk 321 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 30812 Z= 0.548 Angle : 0.818 20.682 41933 Z= 0.432 Chirality : 0.051 0.367 4762 Planarity : 0.006 0.069 5411 Dihedral : 9.246 104.270 4609 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.92 % Favored : 89.03 % Rotamer: Outliers : 4.88 % Allowed : 17.15 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % 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: -2.04 (0.13), residues: 3819 helix: 0.52 (0.19), residues: 720 sheet: -1.95 (0.17), residues: 737 loop : -1.82 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 39 HIS 0.007 0.002 HIS B1083 PHE 0.033 0.003 PHE A 559 TYR 0.041 0.003 TYR B 170 ARG 0.012 0.001 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 67 time to evaluate : 3.336 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 110 LEU cc_start: -0.0724 (OUTLIER) cc_final: -0.1348 (tt) REVERT: A 282 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7117 (m110) REVERT: A 415 THR cc_start: 0.4186 (OUTLIER) cc_final: 0.3750 (p) REVERT: A 489 TYR cc_start: 0.0955 (OUTLIER) cc_final: 0.0083 (t80) REVERT: A 498 ARG cc_start: 0.5274 (OUTLIER) cc_final: 0.4919 (mtm180) REVERT: A 692 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7594 (tp) REVERT: A 740 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: A 855 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: A 1119 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8036 (p0) REVERT: B 125 ASN cc_start: 0.5620 (OUTLIER) cc_final: 0.4959 (m110) REVERT: B 133 PHE cc_start: 0.1688 (OUTLIER) cc_final: 0.0769 (t80) REVERT: B 153 MET cc_start: 0.5486 (tpt) cc_final: 0.5123 (tpt) REVERT: B 172 SER cc_start: 0.2250 (OUTLIER) cc_final: -0.0888 (p) REVERT: B 204 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: B 277 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6462 (mm) REVERT: B 512 VAL cc_start: -0.2751 (OUTLIER) cc_final: -0.3102 (m) REVERT: B 573 THR cc_start: 0.1857 (OUTLIER) cc_final: 0.0103 (t) REVERT: C 154 GLU cc_start: 0.4036 (OUTLIER) cc_final: 0.3789 (tp30) REVERT: C 167 THR cc_start: 0.0112 (OUTLIER) cc_final: -0.1710 (t) REVERT: C 242 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7224 (tt) REVERT: C 258 TRP cc_start: 0.4812 (OUTLIER) cc_final: 0.3448 (p90) REVERT: C 559 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5909 (t80) REVERT: C 693 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6172 (pp) REVERT: C 697 MET cc_start: 0.7235 (tmm) cc_final: 0.7015 (tmm) REVERT: D 100 ARG cc_start: 0.2804 (OUTLIER) cc_final: 0.2482 (mmm160) REVERT: E 4 MET cc_start: 0.5458 (pmm) cc_final: 0.4712 (pmm) REVERT: G 32 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.1887 (p-90) outliers start: 162 outliers final: 119 residues processed: 221 average time/residue: 0.4017 time to fit residues: 146.9862 Evaluate side-chains 206 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 63 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 376 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 30812 Z= 0.306 Angle : 0.671 15.128 41933 Z= 0.346 Chirality : 0.047 0.372 4762 Planarity : 0.005 0.067 5411 Dihedral : 8.876 102.867 4606 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.19 % Allowed : 17.88 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3819 helix: 0.81 (0.19), residues: 723 sheet: -1.91 (0.17), residues: 754 loop : -1.70 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 32 HIS 0.005 0.001 HIS A1058 PHE 0.020 0.002 PHE B 392 TYR 0.024 0.002 TYR B 170 ARG 0.011 0.001 ARG F 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 65 time to evaluate : 3.685 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 110 LEU cc_start: -0.0785 (OUTLIER) cc_final: -0.1367 (tt) REVERT: A 282 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7181 (m110) REVERT: A 415 THR cc_start: 0.4104 (OUTLIER) cc_final: 0.3685 (p) REVERT: A 489 TYR cc_start: 0.0998 (OUTLIER) cc_final: 0.0051 (t80) REVERT: A 498 ARG cc_start: 0.5283 (OUTLIER) cc_final: 0.4871 (mtm180) REVERT: A 692 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7576 (tp) REVERT: A 740 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: A 855 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: A 1119 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7923 (p0) REVERT: B 133 PHE cc_start: 0.1957 (OUTLIER) cc_final: 0.1000 (t80) REVERT: B 172 SER cc_start: 0.1591 (OUTLIER) cc_final: -0.1028 (p) REVERT: B 204 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.5166 (m-80) REVERT: B 512 VAL cc_start: -0.3401 (OUTLIER) cc_final: -0.3682 (m) REVERT: B 573 THR cc_start: 0.0890 (OUTLIER) cc_final: -0.1313 (t) REVERT: C 154 GLU cc_start: 0.3824 (OUTLIER) cc_final: 0.3592 (tp30) REVERT: C 167 THR cc_start: -0.0158 (OUTLIER) cc_final: -0.1932 (t) REVERT: C 242 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7196 (tt) REVERT: C 258 TRP cc_start: 0.4777 (OUTLIER) cc_final: 0.3484 (p90) REVERT: C 559 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5180 (t80) REVERT: C 693 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6234 (pp) REVERT: C 902 MET cc_start: 0.8072 (tpp) cc_final: 0.7845 (tpp) REVERT: E 4 MET cc_start: 0.5341 (pmm) cc_final: 0.4744 (pmm) REVERT: F 100 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6026 (mmp-170) REVERT: G 32 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.1636 (p-90) REVERT: G 70 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4645 (pp20) outliers start: 139 outliers final: 111 residues processed: 197 average time/residue: 0.4143 time to fit residues: 135.4316 Evaluate side-chains 197 residues out of total 3317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 63 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1054 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 24 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 90 HIS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 32 TRP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 300 optimal weight: 0.0020 chunk 125 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.085720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.059397 restraints weight = 230732.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.059268 restraints weight = 218294.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.058993 restraints weight = 204538.031| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30812 Z= 0.245 Angle : 0.630 12.909 41933 Z= 0.322 Chirality : 0.046 0.371 4762 Planarity : 0.005 0.058 5411 Dihedral : 8.628 101.462 4606 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.95 % Allowed : 18.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3819 helix: 1.00 (0.19), residues: 726 sheet: -1.82 (0.17), residues: 754 loop : -1.61 (0.13), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 109 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.002 PHE B 168 TYR 0.020 0.002 TYR B 170 ARG 0.008 0.000 ARG F 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.35 seconds wall clock time: 95 minutes 33.58 seconds (5733.58 seconds total)