Starting phenix.real_space_refine on Sun Feb 18 05:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3m_34469/02_2024/8h3m_34469.pdb" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13420 2.51 5 N 3458 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20936 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7039 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 47, 'TRANS': 862} Chain breaks: 10 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 255 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain breaks: 3 Chain: "B" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5883 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 40, 'TRANS': 722} Chain breaks: 13 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 7213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7213 Classifications: {'peptide': 930} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 48, 'TRANS': 881} Chain breaks: 13 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "H" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain breaks: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.23, per 1000 atoms: 0.54 Number of scatterers: 20936 At special positions: 0 Unit cell: (131.6, 119.568, 168.448, 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 88 16.00 O 3970 8.00 N 3458 7.00 C 13420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " 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=2.02 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 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 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 A1074 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 717 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 717 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 717 " Time building additional restraints: 8.69 Conformation dependent library (CDL) restraints added in 4.0 seconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4998 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 41 sheets defined 28.0% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... 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 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.747A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.517A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.528A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.067A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.104A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.933A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.509A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.513A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.528A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.076A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.067A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.687A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.019A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.763A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.680A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.901A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.982A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.953A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.148A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.736A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.752A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.127A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.842A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.772A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.497A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.080A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.413A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.649A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.445A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.552A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.947A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB9, first strand: chain 'B' and resid 170 through 171 removed outlier: 3.563A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.337A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC4, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.207A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.620A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.454A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.660A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.154A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.033A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.568A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.361A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.449A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1094 through 1097 961 hydrogen bonds defined for protein. 2592 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: 9.27 Time building geometry restraints manager: 9.27 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: 6624 1.35 - 1.48: 5598 1.48 - 1.60: 9056 1.60 - 1.73: 0 1.73 - 1.86: 113 Bond restraints: 21391 Sorted by residual: bond pdb=" N ASN A1108 " pdb=" CA ASN A1108 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.22e-02 6.72e+03 8.36e+00 bond pdb=" CG PRO C 426 " pdb=" CD PRO C 426 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.15e+00 bond pdb=" N GLN A1106 " pdb=" CA GLN A1106 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.34e-02 5.57e+03 6.15e+00 bond pdb=" N ARG A1107 " pdb=" CA ARG A1107 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.75e+00 bond pdb=" CA ASN A 121 " pdb=" CB ASN A 121 " ideal model delta sigma weight residual 1.525 1.556 -0.031 1.29e-02 6.01e+03 5.74e+00 ... (remaining 21386 not shown) Histogram of bond angle deviations from ideal: 93.11 - 101.35: 28 101.35 - 109.59: 2303 109.59 - 117.82: 13791 117.82 - 126.06: 12716 126.06 - 134.30: 257 Bond angle restraints: 29095 Sorted by residual: angle pdb=" N PRO C 426 " pdb=" CD PRO C 426 " pdb=" CG PRO C 426 " ideal model delta sigma weight residual 103.20 93.11 10.09 1.50e+00 4.44e-01 4.52e+01 angle pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 112.00 102.79 9.21 1.40e+00 5.10e-01 4.33e+01 angle pdb=" CA PRO C 426 " pdb=" CB PRO C 426 " pdb=" CG PRO C 426 " ideal model delta sigma weight residual 104.50 94.79 9.71 1.90e+00 2.77e-01 2.61e+01 angle pdb=" C GLU B 619 " pdb=" CA GLU B 619 " pdb=" CB GLU B 619 " ideal model delta sigma weight residual 109.29 115.76 -6.47 1.51e+00 4.39e-01 1.83e+01 angle pdb=" CA PRO C 426 " pdb=" N PRO C 426 " pdb=" CD PRO C 426 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 ... (remaining 29090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 11771 20.74 - 41.48: 933 41.48 - 62.22: 224 62.22 - 82.96: 48 82.96 - 103.70: 15 Dihedral angle restraints: 12991 sinusoidal: 5263 harmonic: 7728 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 0.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -16.94 -69.06 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 30.18 62.82 1 1.00e+01 1.00e-02 5.21e+01 ... (remaining 12988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3412 0.161 - 0.322: 1 0.322 - 0.483: 2 0.483 - 0.644: 0 0.644 - 0.805: 2 Chirality restraints: 3417 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 3414 not shown) Planarity restraints: 3719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 521 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.006 2.00e-02 2.50e+03 2.30e-02 6.61e+00 pdb=" CG ASN A1098 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.002 2.00e-02 2.50e+03 2.27e-02 6.45e+00 pdb=" CG ASN A 282 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " -0.025 2.00e-02 2.50e+03 ... (remaining 3716 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2562 2.75 - 3.29: 19722 3.29 - 3.83: 35303 3.83 - 4.36: 42239 4.36 - 4.90: 72026 Nonbonded interactions: 171852 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.218 2.440 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.227 2.520 nonbonded pdb=" OD2 ASP C 578 " pdb=" OG1 THR C 581 " model vdw 2.233 2.440 nonbonded pdb=" NH1 ARG C 815 " pdb=" OD1 ASP C 820 " model vdw 2.235 2.520 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.269 2.440 ... (remaining 171847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 108 or resid 116 through 130 or resid 168 throu \ gh 375 or resid 378 through 495 or resid 498 or resid 507 through 563 or (resid \ 564 and (name N or name CA or name C or name O or name CB )) or resid 565 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 620 or resid 629 through 635 or resid 641 through 675 or resid \ 690 through 826 or resid 848 through 1106 or (resid 1107 and (name N or name CA \ or name C or name O or name CB )) or resid 1108 through 1138 or resid 1302 thro \ ugh 1308)) selection = (chain 'C' and (resid 27 through 404 or resid 429 through 443 or resid 451 or re \ sid 454 or resid 463 or resid 508 through 1138 or resid 1301 through 1307)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.650 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 59.040 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 0.091 21391 Z= 0.232 Angle : 0.646 12.783 29095 Z= 0.358 Chirality : 0.050 0.805 3417 Planarity : 0.005 0.128 3697 Dihedral : 16.222 103.698 7903 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.58 % Favored : 96.14 % Rotamer: Outliers : 2.03 % Allowed : 16.77 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2568 helix: 2.05 (0.21), residues: 614 sheet: 0.37 (0.20), residues: 582 loop : -1.21 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.036 0.001 PHE B 592 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6025 (pptt) cc_final: 0.5125 (pptt) REVERT: B 309 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7843 (mm-30) outliers start: 46 outliers final: 38 residues processed: 234 average time/residue: 1.0287 time to fit residues: 283.1278 Evaluate side-chains 225 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 240 optimal weight: 0.3980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 394 ASN A 957 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 762 GLN C 532 ASN C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21391 Z= 0.182 Angle : 0.555 7.312 29095 Z= 0.294 Chirality : 0.048 0.600 3417 Planarity : 0.004 0.061 3697 Dihedral : 7.522 71.358 3326 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.78 % Favored : 95.95 % Rotamer: Outliers : 2.96 % Allowed : 15.93 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2568 helix: 2.47 (0.20), residues: 609 sheet: 0.49 (0.20), residues: 580 loop : -1.12 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A1083 PHE 0.028 0.001 PHE B 592 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 188 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: A 1045 LYS cc_start: 0.7691 (tppp) cc_final: 0.7321 (tptt) REVERT: A 1125 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7217 (m110) REVERT: B 309 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 965 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: C 467 ASP cc_start: 0.5876 (t70) cc_final: 0.5312 (m-30) REVERT: C 607 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8023 (mt0) outliers start: 67 outliers final: 36 residues processed: 234 average time/residue: 1.0024 time to fit residues: 276.6721 Evaluate side-chains 218 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 703 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 21391 Z= 0.342 Angle : 0.656 8.560 29095 Z= 0.347 Chirality : 0.053 0.769 3417 Planarity : 0.005 0.050 3697 Dihedral : 6.845 59.156 3302 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.67 % Favored : 95.05 % Rotamer: Outliers : 3.84 % Allowed : 15.45 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2568 helix: 2.26 (0.20), residues: 607 sheet: 0.42 (0.20), residues: 586 loop : -1.25 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 633 HIS 0.004 0.001 HIS A1083 PHE 0.025 0.002 PHE B 592 TYR 0.018 0.002 TYR A1067 ARG 0.004 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 190 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: A 973 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8411 (pp) REVERT: A 1107 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7885 (mtt180) REVERT: B 309 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7823 (mm-30) REVERT: C 338 PHE cc_start: 0.7449 (m-80) cc_final: 0.7077 (m-10) REVERT: C 460 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.6114 (m-40) REVERT: C 467 ASP cc_start: 0.5818 (t70) cc_final: 0.4999 (t0) REVERT: C 607 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: C 675 GLN cc_start: 0.5989 (OUTLIER) cc_final: 0.5082 (pt0) REVERT: C 856 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8129 (mtpp) REVERT: C 973 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6860 (tp) outliers start: 87 outliers final: 53 residues processed: 249 average time/residue: 0.9512 time to fit residues: 281.8713 Evaluate side-chains 241 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 180 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 256 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 957 GLN B 87 ASN B 957 GLN C 394 ASN C 532 ASN C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21391 Z= 0.250 Angle : 0.588 8.058 29095 Z= 0.312 Chirality : 0.050 0.733 3417 Planarity : 0.004 0.047 3697 Dihedral : 6.414 59.723 3300 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 3.66 % Allowed : 16.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2568 helix: 2.37 (0.20), residues: 614 sheet: 0.38 (0.21), residues: 571 loop : -1.23 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 633 HIS 0.006 0.001 HIS A1083 PHE 0.027 0.002 PHE B 592 TYR 0.018 0.002 TYR A1067 ARG 0.003 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 192 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.5064 (mt) REVERT: A 392 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: A 973 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (pp) REVERT: A 1107 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7825 (mtt180) REVERT: B 309 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7869 (mm-30) REVERT: C 338 PHE cc_start: 0.7503 (m-80) cc_final: 0.7125 (m-10) REVERT: C 467 ASP cc_start: 0.5817 (t70) cc_final: 0.5038 (t0) REVERT: C 607 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: C 675 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.4985 (pt0) REVERT: C 856 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8144 (mtpp) REVERT: C 973 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6769 (tp) REVERT: C 1113 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7555 (mm110) outliers start: 83 outliers final: 49 residues processed: 253 average time/residue: 0.9788 time to fit residues: 293.9387 Evaluate side-chains 243 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 0 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 641 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21391 Z= 0.197 Angle : 0.558 8.964 29095 Z= 0.295 Chirality : 0.049 0.692 3417 Planarity : 0.004 0.044 3697 Dihedral : 6.142 59.858 3299 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.93 % Favored : 95.83 % Rotamer: Outliers : 3.40 % Allowed : 16.86 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2568 helix: 2.45 (0.20), residues: 619 sheet: 0.43 (0.21), residues: 571 loop : -1.19 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 191 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: B 309 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 740 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8240 (tpt) REVERT: C 338 PHE cc_start: 0.7504 (m-80) cc_final: 0.7116 (m-10) REVERT: C 467 ASP cc_start: 0.5844 (t70) cc_final: 0.5065 (t0) REVERT: C 607 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: C 973 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6712 (tp) REVERT: C 1113 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7690 (mm110) outliers start: 77 outliers final: 47 residues processed: 247 average time/residue: 0.9423 time to fit residues: 277.7372 Evaluate side-chains 240 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN C 450 ASN C 532 ASN C 641 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21391 Z= 0.201 Angle : 0.555 8.169 29095 Z= 0.293 Chirality : 0.048 0.635 3417 Planarity : 0.004 0.047 3697 Dihedral : 5.876 57.681 3298 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.82 % Favored : 95.95 % Rotamer: Outliers : 4.06 % Allowed : 16.73 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2568 helix: 2.47 (0.20), residues: 620 sheet: 0.45 (0.20), residues: 589 loop : -1.17 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.004 0.001 HIS C1101 PHE 0.030 0.001 PHE B 592 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 195 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: A 403 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.4852 (ptm-80) REVERT: A 675 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.5904 (tt0) REVERT: B 309 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7861 (mm-30) REVERT: B 740 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8268 (tpt) REVERT: C 338 PHE cc_start: 0.7560 (m-80) cc_final: 0.7177 (m-10) REVERT: C 467 ASP cc_start: 0.5785 (t70) cc_final: 0.4937 (p0) REVERT: C 607 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: C 856 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8784 (mmtp) REVERT: C 1113 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7729 (mm110) outliers start: 92 outliers final: 55 residues processed: 265 average time/residue: 0.9410 time to fit residues: 296.7590 Evaluate side-chains 246 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN C 532 ASN C 641 ASN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21391 Z= 0.208 Angle : 0.556 8.730 29095 Z= 0.293 Chirality : 0.049 0.687 3417 Planarity : 0.004 0.051 3697 Dihedral : 5.769 58.054 3298 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.09 % Favored : 95.68 % Rotamer: Outliers : 3.62 % Allowed : 17.12 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2568 helix: 2.49 (0.20), residues: 616 sheet: 0.47 (0.20), residues: 589 loop : -1.15 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.004 0.001 HIS C1101 PHE 0.031 0.001 PHE B 592 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 192 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 403 ARG cc_start: 0.5319 (OUTLIER) cc_final: 0.4866 (ptm-80) REVERT: A 675 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.5910 (tt0) REVERT: A 1107 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7847 (mtt180) REVERT: B 740 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8239 (tpt) REVERT: C 101 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5805 (tp) REVERT: C 338 PHE cc_start: 0.7547 (m-80) cc_final: 0.7155 (m-10) REVERT: C 467 ASP cc_start: 0.5765 (t70) cc_final: 0.4946 (p0) REVERT: C 607 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: C 619 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: C 856 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8785 (mmtp) REVERT: C 1113 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7730 (mm110) outliers start: 82 outliers final: 53 residues processed: 255 average time/residue: 0.9625 time to fit residues: 292.2075 Evaluate side-chains 250 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 354 ASN A 394 ASN A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 641 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 21391 Z= 0.325 Angle : 0.638 8.947 29095 Z= 0.336 Chirality : 0.052 0.718 3417 Planarity : 0.005 0.056 3697 Dihedral : 6.052 59.522 3292 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.71 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 17.26 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2568 helix: 2.32 (0.20), residues: 610 sheet: 0.40 (0.21), residues: 585 loop : -1.21 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 633 HIS 0.006 0.001 HIS C1101 PHE 0.031 0.002 PHE B 592 TYR 0.018 0.002 TYR C1067 ARG 0.003 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 193 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: A 1107 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7884 (mtt180) REVERT: B 740 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8281 (tpt) REVERT: B 820 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: C 101 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5900 (tp) REVERT: C 206 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7975 (tttp) REVERT: C 338 PHE cc_start: 0.7467 (m-80) cc_final: 0.7052 (m-10) REVERT: C 467 ASP cc_start: 0.5684 (t70) cc_final: 0.4904 (p0) REVERT: C 607 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: C 856 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8774 (mmtp) REVERT: C 1113 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7514 (mm110) outliers start: 83 outliers final: 57 residues processed: 255 average time/residue: 0.9989 time to fit residues: 301.7511 Evaluate side-chains 253 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 187 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain H residue 100 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 103 optimal weight: 0.0030 chunk 186 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 394 ASN C 532 ASN C 641 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21391 Z= 0.177 Angle : 0.543 7.927 29095 Z= 0.285 Chirality : 0.048 0.627 3417 Planarity : 0.004 0.046 3697 Dihedral : 5.551 59.419 3292 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.50 % Favored : 96.26 % Rotamer: Outliers : 2.74 % Allowed : 18.40 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2568 helix: 2.53 (0.20), residues: 619 sheet: 0.48 (0.20), residues: 585 loop : -1.14 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS A1083 PHE 0.032 0.001 PHE B 592 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 309 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 206 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7906 (tttp) REVERT: C 338 PHE cc_start: 0.7455 (m-80) cc_final: 0.7049 (m-10) REVERT: C 467 ASP cc_start: 0.5790 (t70) cc_final: 0.4956 (p0) REVERT: C 607 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 856 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8748 (mmtp) REVERT: C 1113 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7699 (mm110) outliers start: 62 outliers final: 43 residues processed: 237 average time/residue: 0.9451 time to fit residues: 267.9059 Evaluate side-chains 234 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 354 ASN A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 641 ASN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21391 Z= 0.215 Angle : 0.566 7.944 29095 Z= 0.298 Chirality : 0.049 0.653 3417 Planarity : 0.004 0.048 3697 Dihedral : 5.551 58.490 3290 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.28 % Favored : 95.48 % Rotamer: Outliers : 2.56 % Allowed : 18.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2568 helix: 2.52 (0.20), residues: 614 sheet: 0.48 (0.20), residues: 581 loop : -1.14 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.004 0.001 HIS C1101 PHE 0.029 0.001 PHE B 592 TYR 0.018 0.002 TYR A1067 ARG 0.005 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 185 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: A 1107 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7864 (mtt180) REVERT: B 309 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 740 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8218 (tpt) REVERT: C 206 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7880 (tttp) REVERT: C 467 ASP cc_start: 0.5740 (t70) cc_final: 0.4928 (p0) REVERT: C 607 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: C 856 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8755 (mmtp) REVERT: C 1113 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7733 (mm110) REVERT: H 34 MET cc_start: 0.3955 (mmm) cc_final: 0.3719 (mmm) outliers start: 58 outliers final: 45 residues processed: 225 average time/residue: 1.0205 time to fit residues: 272.2435 Evaluate side-chains 234 residues out of total 2337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 182 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 210 optimal weight: 0.0670 chunk 88 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 239 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111524 restraints weight = 23900.131| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.74 r_work: 0.3039 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21391 Z= 0.179 Angle : 0.552 8.356 29095 Z= 0.290 Chirality : 0.048 0.688 3417 Planarity : 0.004 0.047 3697 Dihedral : 5.460 58.857 3289 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.62 % Favored : 96.14 % Rotamer: Outliers : 2.47 % Allowed : 18.98 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2568 helix: 2.55 (0.20), residues: 619 sheet: 0.50 (0.20), residues: 585 loop : -1.09 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 353 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE B 592 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG A 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6594.07 seconds wall clock time: 119 minutes 25.71 seconds (7165.71 seconds total)