Starting phenix.real_space_refine on Fri Apr 12 00:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l3n_23156/04_2024/7l3n_23156.pdb" } resolution = 3.27 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= 0.024 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 105 5.16 5 C 15370 2.51 5 N 3981 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24118 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6383 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 44, 'TRANS': 775} Chain breaks: 9 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7813 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 8 Chain: "C" Number of atoms: 7847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7847 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 54, 'TRANS': 950} Chain breaks: 8 Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.25, per 1000 atoms: 0.51 Number of scatterers: 24118 At special positions: 0 Unit cell: (181.131, 138.204, 140.298, 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 105 16.00 O 4662 8.00 N 3981 7.00 C 15370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 717 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1134 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C 801 " Time building additional restraints: 9.89 Conformation dependent library (CDL) restraints added in 3.9 seconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5722 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 50 sheets defined 25.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.788A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.495A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.588A 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 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.579A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.548A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.808A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.319A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 984 removed outlier: 3.677A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.719A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.572A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.578A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.549A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.260A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.653A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 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: 4.296A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.258A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.797A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.136A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.237A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) 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: 5.185A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.728A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.677A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.565A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.014A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.519A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.890A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.562A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.649A 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 913 through 919 removed outlier: 3.517A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.649A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.285A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 109 removed outlier: 5.106A pdb=" N TYR D 107 " --> pdb=" O ARG D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.692A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.817A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.969A 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: 3.530A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.976A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.285A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.147A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.050A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.937A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.738A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.851A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.078A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.097A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.288A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.988A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A 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: 4.923A 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: 8.198A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.169A pdb=" N ARG C 34 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU C 223 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 52 removed outlier: 4.102A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.123A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.529A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.889A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.839A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.846A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.021A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.410A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.804A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.512A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.614A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.490A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2739 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: 12.37 Time building geometry restraints manager: 10.70 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: 7740 1.35 - 1.47: 6226 1.47 - 1.60: 10549 1.60 - 1.72: 2 1.72 - 1.85: 133 Bond restraints: 24650 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 1.254 0.249 3.40e-02 8.65e+02 5.36e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C1 NAG B1303 " pdb=" C2 NAG B1303 " ideal model delta sigma weight residual 1.532 1.598 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.29e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.22e+00 ... (remaining 24645 not shown) Histogram of bond angle deviations from ideal: 87.77 - 97.03: 2 97.03 - 106.30: 685 106.30 - 115.56: 15180 115.56 - 124.83: 17336 124.83 - 134.09: 335 Bond angle restraints: 33538 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 87.77 15.43 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 102.51 9.49 1.40e+00 5.10e-01 4.60e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 127.69 -13.29 2.30e+00 1.89e-01 3.34e+01 angle pdb=" C SER E 30 " pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 117.23 109.62 7.61 1.36e+00 5.41e-01 3.13e+01 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 95.28 9.22 1.90e+00 2.77e-01 2.35e+01 ... (remaining 33533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13748 17.91 - 35.83: 982 35.83 - 53.74: 207 53.74 - 71.66: 45 71.66 - 89.57: 29 Dihedral angle restraints: 15011 sinusoidal: 6131 harmonic: 8880 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -171.22 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -169.08 83.08 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.11 69.11 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 15008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3618 0.097 - 0.195: 273 0.195 - 0.292: 2 0.292 - 0.389: 0 0.389 - 0.487: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA CYS C 525 " pdb=" N CYS C 525 " pdb=" C CYS C 525 " pdb=" CB CYS C 525 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3891 not shown) Planarity restraints: 4331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.080 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO B 384 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 987 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 94 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO E 95 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.038 5.00e-02 4.00e+02 ... (remaining 4328 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 231 2.61 - 3.18: 20956 3.18 - 3.76: 35111 3.76 - 4.33: 49335 4.33 - 4.90: 83109 Nonbonded interactions: 188742 Sorted by model distance: nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.041 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.108 2.440 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.134 2.440 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.147 2.440 ... (remaining 188737 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 'B' and (resid 27 through 95 or resid 99 through 140 or resid 157 through \ 620 or resid 641 through 1146 or resid 1301 through 1304)) selection = (chain 'C' and (resid 27 through 66 or resid 81 through 209 or resid 217 through \ 243 or resid 264 through 1146 or resid 1301 through 1304)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.780 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 66.350 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.249 24650 Z= 0.324 Angle : 0.755 15.433 33538 Z= 0.407 Chirality : 0.051 0.487 3894 Planarity : 0.006 0.115 4312 Dihedral : 13.498 89.573 9178 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -0.76 (0.14), residues: 2996 helix: -0.33 (0.18), residues: 628 sheet: 0.59 (0.18), residues: 733 loop : -1.09 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 PHE 0.030 0.002 PHE A 140 TYR 0.047 0.002 TYR B 453 ARG 0.041 0.004 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.5248 (m-90) cc_final: 0.5039 (m-90) REVERT: B 172 SER cc_start: 0.6837 (t) cc_final: 0.6624 (p) REVERT: C 882 ILE cc_start: 0.8679 (mt) cc_final: 0.8394 (mt) REVERT: D 20 VAL cc_start: 0.9013 (t) cc_final: 0.8781 (t) REVERT: D 107 TYR cc_start: 0.5519 (p90) cc_final: 0.5280 (p90) outliers start: 1 outliers final: 0 residues processed: 535 average time/residue: 0.3512 time to fit residues: 297.0419 Evaluate side-chains 278 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 481 ASN B 493 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1010 GLN B1083 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 79 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24650 Z= 0.217 Angle : 0.663 9.391 33538 Z= 0.343 Chirality : 0.048 0.398 3894 Planarity : 0.005 0.051 4312 Dihedral : 6.485 59.451 3720 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 10.49 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -0.00 (0.14), residues: 2996 helix: 0.77 (0.20), residues: 636 sheet: 0.86 (0.18), residues: 695 loop : -0.68 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.006 0.001 HIS B1083 PHE 0.029 0.002 PHE A 329 TYR 0.024 0.002 TYR D 108 ARG 0.007 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.5334 (m-90) cc_final: 0.5005 (m-90) REVERT: B 229 LEU cc_start: 0.6951 (mp) cc_final: 0.6612 (mp) REVERT: B 856 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7282 (p0) REVERT: C 385 THR cc_start: 0.8887 (p) cc_final: 0.8687 (t) REVERT: C 392 PHE cc_start: 0.6359 (m-10) cc_final: 0.5663 (m-10) REVERT: C 878 LEU cc_start: 0.8113 (mt) cc_final: 0.7881 (mt) REVERT: E 30 SER cc_start: 0.6835 (t) cc_final: 0.6623 (t) outliers start: 52 outliers final: 27 residues processed: 323 average time/residue: 0.3362 time to fit residues: 178.5013 Evaluate side-chains 265 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 237 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 0.2980 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 481 ASN B 544 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 703 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C1010 GLN D 39 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24650 Z= 0.246 Angle : 0.637 9.479 33538 Z= 0.327 Chirality : 0.047 0.387 3894 Planarity : 0.005 0.068 4312 Dihedral : 5.659 56.211 3720 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.81 % Allowed : 12.51 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 0.05 (0.15), residues: 2996 helix: 0.83 (0.20), residues: 658 sheet: 0.70 (0.18), residues: 725 loop : -0.59 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS C1064 PHE 0.024 0.002 PHE B 802 TYR 0.023 0.002 TYR E 86 ARG 0.010 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ASN cc_start: 0.7468 (t0) cc_final: 0.7010 (p0) REVERT: A 1051 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 104 TRP cc_start: 0.5523 (m-90) cc_final: 0.5151 (m-90) REVERT: B 725 GLU cc_start: 0.6709 (pt0) cc_final: 0.6135 (pt0) REVERT: B 1066 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8233 (p) REVERT: C 385 THR cc_start: 0.8978 (p) cc_final: 0.8768 (t) REVERT: D 121 VAL cc_start: 0.5912 (OUTLIER) cc_final: 0.5390 (p) outliers start: 75 outliers final: 36 residues processed: 286 average time/residue: 0.3477 time to fit residues: 161.3566 Evaluate side-chains 214 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 314 GLN B 448 ASN B 481 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 79 GLN E 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 24650 Z= 0.441 Angle : 0.732 9.768 33538 Z= 0.378 Chirality : 0.051 0.435 3894 Planarity : 0.005 0.054 4312 Dihedral : 5.904 55.684 3720 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.82 % Allowed : 13.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2996 helix: 0.58 (0.20), residues: 667 sheet: 0.44 (0.18), residues: 719 loop : -0.71 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 35 HIS 0.006 0.001 HIS A1064 PHE 0.034 0.002 PHE C 797 TYR 0.048 0.002 TYR C 369 ARG 0.007 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 169 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 104 TRP cc_start: 0.5598 (m-90) cc_final: 0.5276 (m-90) REVERT: B 544 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7769 (p0) REVERT: C 380 TYR cc_start: 0.7457 (m-10) cc_final: 0.7187 (m-10) outliers start: 102 outliers final: 56 residues processed: 260 average time/residue: 0.3508 time to fit residues: 149.8782 Evaluate side-chains 205 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 147 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 0.0970 chunk 250 optimal weight: 0.5980 chunk 203 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 263 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 481 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24650 Z= 0.170 Angle : 0.577 10.379 33538 Z= 0.293 Chirality : 0.046 0.439 3894 Planarity : 0.004 0.051 4312 Dihedral : 5.313 55.553 3720 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.40 % Allowed : 15.69 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2996 helix: 1.07 (0.20), residues: 670 sheet: 0.51 (0.18), residues: 708 loop : -0.56 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.034 0.001 PHE C 392 TYR 0.021 0.001 TYR D 80 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 166 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.5522 (m-90) cc_final: 0.5186 (m-90) REVERT: C 189 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7734 (pt) outliers start: 64 outliers final: 38 residues processed: 219 average time/residue: 0.3507 time to fit residues: 125.1555 Evaluate side-chains 189 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 294 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 957 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24650 Z= 0.273 Angle : 0.597 15.250 33538 Z= 0.301 Chirality : 0.046 0.449 3894 Planarity : 0.004 0.117 4312 Dihedral : 5.289 54.987 3720 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.51 % Allowed : 16.29 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2996 helix: 1.17 (0.20), residues: 669 sheet: 0.52 (0.19), residues: 696 loop : -0.55 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.004 0.001 HIS C1064 PHE 0.027 0.001 PHE C 392 TYR 0.022 0.001 TYR D 80 ARG 0.005 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 156 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: B 104 TRP cc_start: 0.5557 (m-90) cc_final: 0.5239 (m-90) REVERT: C 189 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7880 (pt) REVERT: D 81 MET cc_start: 0.5649 (tpt) cc_final: 0.5449 (tpt) REVERT: D 112 MET cc_start: 0.4750 (mpp) cc_final: 0.4146 (mpp) outliers start: 67 outliers final: 52 residues processed: 213 average time/residue: 0.3591 time to fit residues: 125.5316 Evaluate side-chains 194 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 20.0000 chunk 33 optimal weight: 0.0040 chunk 167 optimal weight: 0.9980 chunk 214 optimal weight: 0.0980 chunk 166 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 293 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 481 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 804 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24650 Z= 0.159 Angle : 0.559 10.066 33538 Z= 0.283 Chirality : 0.045 0.445 3894 Planarity : 0.004 0.067 4312 Dihedral : 5.075 55.410 3720 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.13 % Allowed : 16.89 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2996 helix: 1.47 (0.21), residues: 658 sheet: 0.58 (0.18), residues: 713 loop : -0.49 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.003 0.000 HIS C1048 PHE 0.028 0.001 PHE B 133 TYR 0.035 0.001 TYR C 160 ARG 0.009 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 993 ILE cc_start: 0.8962 (mm) cc_final: 0.8670 (mt) REVERT: B 104 TRP cc_start: 0.5559 (m-90) cc_final: 0.5229 (m-90) REVERT: C 189 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7941 (pt) REVERT: C 385 THR cc_start: 0.9122 (p) cc_final: 0.8915 (t) REVERT: D 112 MET cc_start: 0.4703 (mpp) cc_final: 0.4217 (mpp) outliers start: 57 outliers final: 43 residues processed: 204 average time/residue: 0.3487 time to fit residues: 116.9825 Evaluate side-chains 191 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.4980 chunk 117 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 186 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 144 optimal weight: 0.0000 chunk 27 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24650 Z= 0.164 Angle : 0.550 9.568 33538 Z= 0.278 Chirality : 0.045 0.447 3894 Planarity : 0.004 0.055 4312 Dihedral : 4.988 55.121 3720 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.21 % Allowed : 16.97 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2996 helix: 1.59 (0.21), residues: 658 sheet: 0.60 (0.18), residues: 715 loop : -0.44 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.003 0.000 HIS A 66 PHE 0.040 0.001 PHE A 329 TYR 0.020 0.001 TYR D 80 ARG 0.007 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 157 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6269 (tp30) REVERT: A 993 ILE cc_start: 0.8938 (mm) cc_final: 0.8644 (mt) REVERT: B 104 TRP cc_start: 0.5584 (m-90) cc_final: 0.5263 (m-90) REVERT: C 189 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7921 (pt) REVERT: D 86 LEU cc_start: 0.5546 (tt) cc_final: 0.5334 (mm) REVERT: D 112 MET cc_start: 0.4689 (mpp) cc_final: 0.4220 (mpp) REVERT: E 49 TYR cc_start: 0.6479 (p90) cc_final: 0.6266 (p90) outliers start: 59 outliers final: 46 residues processed: 207 average time/residue: 0.3620 time to fit residues: 121.6142 Evaluate side-chains 192 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 144 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.3980 chunk 280 optimal weight: 6.9990 chunk 256 optimal weight: 0.4980 chunk 273 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24650 Z= 0.172 Angle : 0.559 9.541 33538 Z= 0.282 Chirality : 0.045 0.441 3894 Planarity : 0.004 0.055 4312 Dihedral : 4.958 55.281 3720 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 17.42 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 2996 helix: 1.62 (0.21), residues: 661 sheet: 0.65 (0.18), residues: 708 loop : -0.43 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.003 0.000 HIS D 105 PHE 0.036 0.001 PHE A 329 TYR 0.021 0.001 TYR D 108 ARG 0.007 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.5836 (tp30) REVERT: A 993 ILE cc_start: 0.8935 (mm) cc_final: 0.8645 (mt) REVERT: B 104 TRP cc_start: 0.5605 (m-90) cc_final: 0.5283 (m-90) REVERT: C 189 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7942 (pt) REVERT: D 112 MET cc_start: 0.4585 (mpp) cc_final: 0.4155 (mpp) outliers start: 58 outliers final: 49 residues processed: 200 average time/residue: 0.3639 time to fit residues: 118.9303 Evaluate side-chains 192 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 901 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 787 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.7011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24650 Z= 0.263 Angle : 0.592 9.579 33538 Z= 0.301 Chirality : 0.046 0.444 3894 Planarity : 0.004 0.054 4312 Dihedral : 5.117 55.241 3720 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.99 % Allowed : 17.45 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2996 helix: 1.45 (0.21), residues: 666 sheet: 0.56 (0.18), residues: 716 loop : -0.40 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.005 0.001 HIS D 105 PHE 0.035 0.001 PHE A 329 TYR 0.023 0.001 TYR B 449 ARG 0.009 0.001 ARG D 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6186 (tp30) REVERT: B 104 TRP cc_start: 0.5575 (m-90) cc_final: 0.5274 (m-90) REVERT: C 189 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8047 (pt) outliers start: 53 outliers final: 46 residues processed: 187 average time/residue: 0.3542 time to fit residues: 107.3262 Evaluate side-chains 181 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 133 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 9.9990 chunk 256 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 241 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 762 GLN B 901 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.098236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068127 restraints weight = 73806.743| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.49 r_work: 0.3128 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24650 Z= 0.160 Angle : 0.562 9.530 33538 Z= 0.283 Chirality : 0.045 0.436 3894 Planarity : 0.004 0.055 4312 Dihedral : 4.942 55.329 3720 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.87 % Allowed : 17.72 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 2996 helix: 1.64 (0.21), residues: 662 sheet: 0.68 (0.18), residues: 714 loop : -0.39 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.002 0.000 HIS C1048 PHE 0.032 0.001 PHE A 329 TYR 0.018 0.001 TYR D 80 ARG 0.008 0.000 ARG D 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.95 seconds wall clock time: 94 minutes 56.88 seconds (5696.88 seconds total)