Starting phenix.real_space_refine on Sun Jul 5 07:32:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gnh_34164/07_2026/8gnh_34164.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16603 2.51 5 N 4333 2.21 5 O 5121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26171 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7816 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 55, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 12, 'ARG:plan': 7, 'TYR:plan': 6, 'TRP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 207 Chain: "B" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8083 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'PHE:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8096 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 56, 'TRANS': 991} Chain breaks: 7 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 903 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 769 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" 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 chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: N Time building chain proxies: 6.48, per 1000 atoms: 0.25 Number of scatterers: 26171 At special positions: 0 Unit cell: (138.205, 139.26, 229.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5121 8.00 N 4333 7.00 C 16603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=2.05 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=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.09 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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 H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25735 O5 NAG A1301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1302 " - " ASN A1098 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A1074 " " NAG B1301 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 165 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6298 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 45 sheets defined 22.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.926A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.538A pdb=" N ALA A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.770A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 782 removed outlier: 4.705A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 898 through 910 removed outlier: 4.464A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.744A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 3.717A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 985 through 1030 removed outlier: 4.796A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.620A pdb=" N THR A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.534A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.115A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.881A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.951A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 759 through 783 removed outlier: 3.903A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.565A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.927A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.517A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.632A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.530A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 941 removed outlier: 4.240A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.728A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.676A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.623A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.967A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 636 removed outlier: 4.082A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.645A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 4.860A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 835 through 840 removed outlier: 3.945A pdb=" N ASP C 839 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.523A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 938 removed outlier: 4.269A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.883A 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 982 removed outlier: 3.670A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1035 removed outlier: 4.105A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.603A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.796A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.607A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.592A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.902A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.630A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.313A 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 702 removed outlier: 6.535A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.801A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.968A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.690A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.690A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 106 removed outlier: 4.822A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.478A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.689A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.427A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.596A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.878A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AC6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC7, first strand: chain 'C' and resid 48 through 53 removed outlier: 7.344A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 63 through 65 removed outlier: 4.169A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.231A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.948A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.938A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.528A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.206A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AD7, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AD8, first strand: chain 'C' and resid 576 through 578 Processing sheet with id=AD9, first strand: chain 'C' and resid 665 through 667 removed outlier: 7.050A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 713 through 719 removed outlier: 6.924A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 713 through 719 removed outlier: 6.924A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.161A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.620A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.620A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA L 84 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 20 through 24 732 hydrogen bonds defined for protein. 1977 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: 5.77 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4325 1.30 - 1.44: 7525 1.44 - 1.59: 14744 1.59 - 1.73: 1 1.73 - 1.88: 138 Bond restraints: 26733 Sorted by residual: bond pdb=" CA PHE A 32 " pdb=" C PHE A 32 " ideal model delta sigma weight residual 1.522 1.431 0.091 1.08e-02 8.57e+03 7.14e+01 bond pdb=" C VAL B1104 " pdb=" O VAL B1104 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.09e-02 8.42e+03 5.44e+01 bond pdb=" CA TYR C 707 " pdb=" C TYR C 707 " ideal model delta sigma weight residual 1.523 1.433 0.090 1.24e-02 6.50e+03 5.28e+01 bond pdb=" CA TYR B 279 " pdb=" C TYR B 279 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.11e-02 8.12e+03 4.53e+01 bond pdb=" CA VAL B1104 " pdb=" C VAL B1104 " ideal model delta sigma weight residual 1.522 1.436 0.086 1.29e-02 6.01e+03 4.48e+01 ... (remaining 26728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 34710 3.28 - 6.56: 1425 6.56 - 9.84: 235 9.84 - 13.12: 59 13.12 - 16.40: 20 Bond angle restraints: 36449 Sorted by residual: angle pdb=" N ILE B 712 " pdb=" CA ILE B 712 " pdb=" C ILE B 712 " ideal model delta sigma weight residual 111.62 126.20 -14.58 7.90e-01 1.60e+00 3.40e+02 angle pdb=" N GLN C 580 " pdb=" CA GLN C 580 " pdb=" C GLN C 580 " ideal model delta sigma weight residual 111.03 96.07 14.96 1.11e+00 8.12e-01 1.82e+02 angle pdb=" N SER A 98 " pdb=" CA SER A 98 " pdb=" C SER A 98 " ideal model delta sigma weight residual 111.81 95.76 16.05 1.44e+00 4.82e-01 1.24e+02 angle pdb=" N SER C 31 " pdb=" CA SER C 31 " pdb=" C SER C 31 " ideal model delta sigma weight residual 113.15 124.84 -11.69 1.19e+00 7.06e-01 9.64e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 111.02 122.78 -11.76 1.22e+00 6.72e-01 9.29e+01 ... (remaining 36444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 13934 17.74 - 35.49: 1250 35.49 - 53.23: 372 53.23 - 70.97: 96 70.97 - 88.71: 39 Dihedral angle restraints: 15691 sinusoidal: 5916 harmonic: 9775 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 15.45 77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -8.81 -77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -159.78 73.78 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 15688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.181: 4301 1.181 - 2.362: 3 2.362 - 3.542: 3 3.542 - 4.723: 0 4.723 - 5.904: 1 Chirality restraints: 4308 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 3.50 -5.90 2.00e-01 2.50e+01 8.71e+02 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 0.58 -2.98 2.00e-01 2.50e+01 2.22e+02 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 0.57 -2.97 2.00e-01 2.50e+01 2.20e+02 ... (remaining 4305 not shown) Planarity restraints: 4714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.311 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG A1301 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.480 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.308 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG B1304 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.452 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.086 2.00e-02 2.50e+03 7.99e-02 7.98e+01 pdb=" CG ASN B 603 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.099 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.097 2.00e-02 2.50e+03 ... (remaining 4711 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 12 2.15 - 2.84: 10832 2.84 - 3.52: 38566 3.52 - 4.21: 61420 4.21 - 4.90: 101597 Nonbonded interactions: 212427 Sorted by model distance: nonbonded pdb=" ND2 ASN A 801 " pdb=" O5 NAG A1301 " model vdw 1.460 3.120 nonbonded pdb=" OD1 ASN B 282 " pdb=" C1 NAG B1306 " model vdw 1.755 2.776 nonbonded pdb=" OD1 ASN C1134 " pdb=" C1 NAG C1302 " model vdw 1.809 3.470 nonbonded pdb=" OD1 ASN B 282 " pdb=" O5 NAG B1306 " model vdw 1.893 3.040 nonbonded pdb=" OD1 ASN A 801 " pdb=" C1 NAG A1301 " model vdw 2.031 3.470 ... (remaining 212422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 131 or (resid 132 through 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 159 or (resid 1 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 172 or resid 186 through 212 or (resid 213 through 214 and (name N or name CA o \ r name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 250 or res \ id 265 through 275 or (resid 276 through 281 and (name N or name CA or name C or \ name O or name CB )) or resid 282 through 318 or (resid 319 and (name N or name \ CA or name C or name O or name CB )) or resid 320 through 326 or (resid 327 thr \ ough 329 and (name N or name CA or name C or name O or name CB )) or resid 330 t \ hrough 334 or (resid 335 and (name N or name CA or name C or name O or name CB ) \ ) or resid 336 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O or name CB )) or resid 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB )) or resid 343 through 345 or (resid 346 and (name N or \ name CA or name C or name O or name CB )) or resid 347 through 363 or (resid 364 \ through 365 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 66 through 367 or (resid 368 and (name N or name CA or name C or name O or name \ CB )) or resid 369 through 387 or (resid 388 and (name N or name CA or name C or \ name O or name CB )) or resid 389 through 428 or (resid 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 452 or (resid 453 and \ (name N or name CA or name C or name O or name CB )) or resid 454 through 460 o \ r (resid 461 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 62 through 516 or (resid 517 and (name N or name CA or name C or name O or name \ CB )) or resid 518 through 527 or (resid 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 through 828 or resid 850 through 981 or (resi \ d 982 and (name N or name CA or name C or name O or name CB )) or resid 983 thro \ ugh 1080 or (resid 1081 and (name N or name CA or name C or name O or name CB )) \ or resid 1082 through 1096 or (resid 1097 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1098 through 1099 or (resid 1100 through 1107 and ( \ name N or name CA or name C or name O or name CB )) or resid 1108 or (resid 1109 \ and (name N or name CA or name C or name O or name CB )) or resid 1110 through \ 1134 or (resid 1135 and (name N or name CA or name C or name O or name CB )) or \ resid 1136 through 1309)) selection = (chain 'B' and (resid 27 through 30 or (resid 31 through 32 and (name N or name \ CA or name C or name O or name CB )) or resid 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 or (resid 36 through 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 54 or (r \ esid 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thr \ ough 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or \ resid 59 through 63 or (resid 64 through 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 95 or (resid 96 and (name N or name CA \ or name C or name O or name CB )) or resid 97 through 100 or (resid 101 through \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throu \ gh 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or \ resid 115 through 117 or (resid 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 194 or (resid 195 and (name N \ or name CA or name C or name O or name CB )) or resid 196 through 200 or (resid \ 201 and (name N or name CA or name C or name O or name CB )) or resid 202 throu \ gh 212 or (resid 213 through 214 and (name N or name CA or name C or name O or n \ ame CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 222 or (resid 223 and (name N or \ name CA or name C or name O or name CB )) or resid 224 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throu \ gh 250 or resid 265 through 326 or (resid 327 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 334 or (resid 335 and (n \ ame N or name CA or name C or name O or name CB )) or resid 336 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 345 or (resid 346 and (name N or name CA or name C or na \ me O or name CB )) or resid 347 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 or (resid 351 through 352 and (n \ ame N or name CA or name C or name O or name CB )) or resid 353 through 391 or ( \ resid 392 and (name N or name CA or name C or name O or name CB )) or resid 393 \ through 399 or (resid 400 and (name N or name CA or name C or name O or name CB \ )) or resid 401 through 408 or (resid 409 and (name N or name CA or name C or na \ me O or name CB )) or resid 410 through 438 or (resid 439 and (name N or name CA \ or name C or name O or name CB )) or resid 440 through 441 or (resid 442 and (n \ ame N or name CA or name C or name O or name CB )) or resid 450 through 496 or ( \ resid 497 through 498 and (name N or name CA or name C or name O or name CB )) o \ r resid 499 through 504 or (resid 505 and (name N or name CA or name C or name O \ or name CB )) or resid 506 through 507 or (resid 508 through 509 and (name N or \ name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 540 or (resi \ d 541 and (name N or name CA or name C or name O or name CB )) or resid 542 thro \ ugh 550 or (resid 551 and (name N or name CA or name C or name O or name CB )) o \ r resid 552 or (resid 553 through 555 and (name N or name CA or name C or name O \ or name CB )) or resid 556 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 or (resid 585 through 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 736 or (resi \ d 737 and (name N or name CA or name C or name O or name CB )) or resid 738 thro \ ugh 815 or (resid 816 and (name N or name CA or name C or name O or name CB )) o \ r resid 817 through 828 or resid 850 through 857 or (resid 858 and (name N or na \ me CA or name C or name O or name CB )) or resid 859 through 1096 or (resid 1097 \ and (name N or name CA or name C or name O or name CB )) or resid 1098 through \ 1099 or (resid 1100 through 1107 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1108 or (resid 1109 and (name N or name CA or name C or name \ O or name CB )) or resid 1110 through 1309)) selection = (chain 'C' and (resid 27 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 35 or (resid 36 through 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 54 or (res \ id 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throu \ gh 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or r \ esid 59 through 63 or (resid 64 through 65 and (name N or name CA or name C or n \ ame O or name CB )) or resid 66 through 95 or (resid 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 through 100 or (resid 101 through 1 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 103 through \ 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or r \ esid 115 through 117 or (resid 118 and (name N or name CA or name C or name O or \ name CB )) or resid 119 through 131 or (resid 132 through 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 159 or (resid 1 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 or (resid 194 through 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 199 or (resid 200 through 201 and ( \ name N or name CA or name C or name O or name CB )) or resid 202 through 213 or \ (resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 222 or (resid 223 and (name N or name CA or name C or name O or name CB \ )) or resid 224 through 236 or (resid 237 and (name N or name CA or name C or n \ ame O or name CB )) or resid 238 or (resid 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB )) or resid 242 through 250 or resid 265 through 275 or \ (resid 276 through 281 and (name N or name CA or name C or name O or name CB )) \ or resid 282 through 318 or (resid 319 and (name N or name CA or name C or name \ O or name CB )) or resid 320 through 339 or (resid 340 and (name N or name CA o \ r name C or name O or name CB )) or resid 341 through 348 or (resid 349 and (nam \ e N or name CA or name C or name O or name CB )) or resid 350 or (resid 351 thro \ ugh 352 and (name N or name CA or name C or name O or name CB )) or resid 353 th \ rough 363 or (resid 364 through 365 and (name N or name CA or name C or name O o \ r name CB )) or resid 366 through 367 or (resid 368 and (name N or name CA or na \ me C or name O or name CB )) or resid 369 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 391 or (resid \ 392 and (name N or name CA or name C or name O or name CB )) or resid 393 throug \ h 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) or \ resid 401 through 402 or (resid 403 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 428 or (resid 429 and (name N \ or name CA or name C or name O or name CB )) or resid 430 through 438 or (resid \ 439 and (name N or name CA or name C or name O or name CB )) or resid 440 throug \ h 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 452 or (resid 453 and (name N or name CA or name C or name O o \ r name CB )) or resid 454 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 494 or (resid 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throug \ h 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 507 or (resid 508 through 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 514 or (resid 515 through 517 \ and (name N or name CA or name C or name O or name CB )) or resid 518 through 52 \ 7 or (resid 528 and (name N or name CA or name C or name O or name CB )) or resi \ d 529 through 540 or (resid 541 and (name N or name CA or name C or name O or na \ me CB )) or resid 542 through 550 or (resid 551 and (name N or name CA or name C \ or name O or name CB )) or resid 552 or (resid 553 through 555 and (name N or n \ ame CA or name C or name O or name CB )) or resid 556 through 582 or (resid 583 \ and (name N or name CA or name C or name O or name CB )) or resid 584 or (resid \ 585 through 586 and (name N or name CA or name C or name O or name CB )) or resi \ d 587 through 815 or (resid 816 and (name N or name CA or name C or name O or na \ me CB )) or resid 817 through 828 or resid 834 or resid 851 through 857 or (resi \ d 858 and (name N or name CA or name C or name O or name CB )) or resid 859 thro \ ugh 981 or (resid 982 and (name N or name CA or name C or name O or name CB )) o \ r resid 983 through 1080 or (resid 1081 and (name N or name CA or name C or name \ O or name CB )) or resid 1082 through 1106 or (resid 1107 and (name N or name C \ A or name C or name O or name CB )) or resid 1108 through 1134 or (resid 1135 an \ d (name N or name CA or name C or name O or name CB )) or resid 1136 through 130 \ 9)) } ncs_group { reference = chain 'D' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 25.930 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.014 0.869 26802 Z= 0.769 Angle : 1.719 48.017 36614 Z= 0.948 Chirality : 0.166 5.904 4308 Planarity : 0.011 0.272 4689 Dihedral : 16.053 88.713 9267 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 49.62 Ramachandran Plot: Outliers : 4.01 % Allowed : 20.32 % Favored : 75.67 % Rotamer: Outliers : 8.96 % Allowed : 3.41 % Favored : 87.62 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.12), residues: 3317 helix: -2.06 (0.17), residues: 675 sheet: -2.98 (0.23), residues: 457 loop : -4.22 (0.11), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 44 TYR 0.082 0.003 TYR A 91 PHE 0.072 0.004 PHE B 643 TRP 0.044 0.004 TRP B 436 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01221 / 0.70 (26733) covalent geometry : angle 1.56439 / 0.92 (36449) SS BOND : bond 0.01206 / 0.58 ( 42) SS BOND : angle 2.51540 / 1.54 ( 84) hydrogen bonds : bond 0.19708 / 13.02 ( 707) hydrogen bonds : angle 9.41120 / 6.17 ( 1977) link_BETA1-4 : bond 0.06591 / 3.31 ( 2) link_BETA1-4 : angle 9.21541 / 5.65 ( 6) link_NAG-ASN : bond 0.20326 / 10.63 ( 25) link_NAG-ASN : angle 15.45600 / 9.92 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 123 time to evaluate : 1.041 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 81 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.5897 (m110) REVERT: A 91 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6278 (p90) REVERT: A 97 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7285 (mtmt) REVERT: A 229 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 325 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 326 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6420 (mt) REVERT: A 429 PHE cc_start: 0.7949 (t80) cc_final: 0.7523 (t80) REVERT: A 453 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 859 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 901 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8906 (tm-30) REVERT: B 215 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4898 (m-30) REVERT: B 304 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8749 (mmtt) REVERT: B 740 MET cc_start: 0.9102 (tpt) cc_final: 0.8675 (tpp) REVERT: B 954 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: B 960 ASN cc_start: 0.8695 (m-40) cc_final: 0.8411 (t0) REVERT: C 86 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 242 LEU cc_start: 0.8606 (mp) cc_final: 0.8010 (mp) REVERT: C 365 TYR cc_start: 0.9417 (m-80) cc_final: 0.9191 (m-80) REVERT: C 582 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9283 (mm) REVERT: C 1031 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: C 1033 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9162 (p) REVERT: L 78 LEU cc_start: -0.1293 (tp) cc_final: -0.1516 (mt) outliers start: 252 outliers final: 132 residues processed: 365 average time/residue: 0.1661 time to fit residues: 99.0653 Evaluate side-chains 225 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 77 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN A1119 ASN B 125 ASN B 134 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 919 ASN B 920 GLN B 954 GLN B1071 GLN B1074 ASN B1106 GLN C 87 ASN C 99 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 544 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN H 39 GLN H 52 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.084189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.057475 restraints weight = 119557.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.059353 restraints weight = 55526.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060551 restraints weight = 35059.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.061261 restraints weight = 26490.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061636 restraints weight = 22380.693| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26802 Z= 0.185 Angle : 0.969 21.660 36614 Z= 0.469 Chirality : 0.057 0.515 4308 Planarity : 0.006 0.071 4689 Dihedral : 10.753 102.524 3864 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.56 % Favored : 85.02 % Rotamer: Outliers : 5.12 % Allowed : 9.96 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.13), residues: 3317 helix: -0.25 (0.20), residues: 694 sheet: -2.88 (0.21), residues: 523 loop : -3.69 (0.11), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 44 TYR 0.031 0.002 TYR A 707 PHE 0.031 0.002 PHE A 59 TRP 0.031 0.002 TRP A 353 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (26733) covalent geometry : angle 0.93184 / 0.46 (36449) SS BOND : bond 0.00440 / 0.25 ( 42) SS BOND : angle 1.81038 / 1.11 ( 84) hydrogen bonds : bond 0.05210 / 3.50 ( 707) hydrogen bonds : angle 6.48413 / 4.25 ( 1977) link_BETA1-4 : bond 0.02530 / 1.23 ( 2) link_BETA1-4 : angle 3.15489 / 1.84 ( 6) link_NAG-ASN : bond 0.00802 / 0.41 ( 25) link_NAG-ASN : angle 5.66942 / 3.68 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 127 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.6854 (m110) REVERT: A 206 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8413 (tptp) REVERT: A 229 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8401 (pp) REVERT: A 429 PHE cc_start: 0.8160 (t80) cc_final: 0.7334 (t80) REVERT: A 587 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6994 (tp) REVERT: A 740 MET cc_start: 0.8323 (tmm) cc_final: 0.7762 (tmm) REVERT: A 802 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8277 (p90) REVERT: B 215 ASP cc_start: 0.5086 (OUTLIER) cc_final: 0.4718 (m-30) REVERT: B 235 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 304 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8705 (mmmt) REVERT: B 380 TYR cc_start: 0.8090 (m-80) cc_final: 0.7833 (m-80) REVERT: B 468 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 740 MET cc_start: 0.9132 (tpt) cc_final: 0.8700 (tpp) REVERT: B 776 LYS cc_start: 0.9333 (tppp) cc_final: 0.9104 (tppt) REVERT: B 960 ASN cc_start: 0.8668 (m-40) cc_final: 0.8420 (t0) REVERT: B 1071 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: C 238 PHE cc_start: 0.8464 (p90) cc_final: 0.8076 (p90) REVERT: C 269 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: C 365 TYR cc_start: 0.9404 (m-80) cc_final: 0.9158 (m-80) REVERT: C 718 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8291 (p90) REVERT: C 921 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8096 (tptt) REVERT: C 1107 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7495 (tpm170) REVERT: L 53 ASN cc_start: 0.6430 (OUTLIER) cc_final: 0.6024 (p0) REVERT: L 78 LEU cc_start: -0.1179 (tp) cc_final: -0.1555 (mt) REVERT: L 97 PHE cc_start: 0.8139 (t80) cc_final: 0.7871 (t80) outliers start: 144 outliers final: 70 residues processed: 262 average time/residue: 0.1664 time to fit residues: 71.8901 Evaluate side-chains 170 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 85 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 266 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 312 optimal weight: 30.0000 chunk 146 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 289 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1135 ASN B 122 ASN B 331 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.080953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054398 restraints weight = 121084.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056853 restraints weight = 63223.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057047 restraints weight = 33955.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057241 restraints weight = 27532.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057331 restraints weight = 27936.932| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26802 Z= 0.230 Angle : 0.885 26.365 36614 Z= 0.428 Chirality : 0.053 0.809 4308 Planarity : 0.006 0.079 4689 Dihedral : 8.458 69.063 3710 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.50 % Favored : 84.26 % Rotamer: Outliers : 4.55 % Allowed : 13.80 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.14), residues: 3317 helix: 0.58 (0.20), residues: 691 sheet: -2.70 (0.20), residues: 585 loop : -3.42 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1019 TYR 0.030 0.002 TYR A 707 PHE 0.021 0.002 PHE L 62 TRP 0.021 0.002 TRP A 353 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (26733) covalent geometry : angle 0.84787 / 0.42 (36449) SS BOND : bond 0.00332 / 0.20 ( 42) SS BOND : angle 1.28238 / 0.79 ( 84) hydrogen bonds : bond 0.04787 / 3.18 ( 707) hydrogen bonds : angle 6.09363 / 3.99 ( 1977) link_BETA1-4 : bond 0.00926 / 0.47 ( 2) link_BETA1-4 : angle 2.35453 / 1.46 ( 6) link_NAG-ASN : bond 0.00784 / 0.38 ( 25) link_NAG-ASN : angle 5.56968 / 3.38 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 91 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.6887 (m110) REVERT: A 206 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8487 (tptp) REVERT: A 229 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 336 CYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6700 (t) REVERT: A 378 LYS cc_start: 0.7984 (tptp) cc_final: 0.7769 (tptp) REVERT: A 421 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: A 429 PHE cc_start: 0.8181 (t80) cc_final: 0.7499 (t80) REVERT: A 433 VAL cc_start: 0.8581 (m) cc_final: 0.8353 (m) REVERT: A 460 ASN cc_start: 0.8928 (p0) cc_final: 0.8465 (m-40) REVERT: A 587 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7305 (tp) REVERT: A 740 MET cc_start: 0.8365 (tmm) cc_final: 0.7682 (tmm) REVERT: A 802 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8105 (p90) REVERT: B 69 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6228 (m-70) REVERT: B 215 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5365 (m-30) REVERT: B 304 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8969 (mmmt) REVERT: B 380 TYR cc_start: 0.8128 (m-80) cc_final: 0.7778 (m-80) REVERT: B 468 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 740 MET cc_start: 0.9257 (tpt) cc_final: 0.8829 (tpp) REVERT: B 869 MET cc_start: 0.8155 (ptm) cc_final: 0.7828 (ptp) REVERT: B 985 ASP cc_start: 0.8254 (p0) cc_final: 0.7946 (p0) REVERT: B 988 GLU cc_start: 0.8791 (mp0) cc_final: 0.8568 (mp0) REVERT: B 1071 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7989 (tp40) REVERT: C 186 PHE cc_start: 0.3292 (t80) cc_final: 0.2949 (t80) REVERT: C 365 TYR cc_start: 0.9485 (m-80) cc_final: 0.9188 (m-10) REVERT: C 387 LEU cc_start: 0.8918 (mt) cc_final: 0.8704 (mm) REVERT: C 697 MET cc_start: 0.8740 (ttp) cc_final: 0.8486 (ttp) REVERT: C 718 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.8384 (p90) REVERT: C 775 ASP cc_start: 0.8792 (t0) cc_final: 0.8485 (t0) REVERT: C 921 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8262 (tptt) REVERT: L 97 PHE cc_start: 0.8228 (t80) cc_final: 0.7880 (t80) outliers start: 128 outliers final: 69 residues processed: 210 average time/residue: 0.1662 time to fit residues: 57.9984 Evaluate side-chains 153 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 70 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 125 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 315 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 644 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.081002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.053835 restraints weight = 119904.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.055558 restraints weight = 57974.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.056667 restraints weight = 37589.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057337 restraints weight = 28894.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.057748 restraints weight = 24585.682| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26802 Z= 0.174 Angle : 0.796 23.037 36614 Z= 0.384 Chirality : 0.050 0.669 4308 Planarity : 0.005 0.079 4689 Dihedral : 7.659 59.132 3692 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.84 % Favored : 86.92 % Rotamer: Outliers : 3.95 % Allowed : 15.26 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.14), residues: 3317 helix: 1.07 (0.21), residues: 680 sheet: -2.47 (0.21), residues: 580 loop : -3.23 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.036 0.001 TYR B 380 PHE 0.020 0.002 PHE B 490 TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (26733) covalent geometry : angle 0.75965 / 0.38 (36449) SS BOND : bond 0.00308 / 0.18 ( 42) SS BOND : angle 1.24778 / 0.74 ( 84) hydrogen bonds : bond 0.04192 / 2.80 ( 707) hydrogen bonds : angle 5.73727 / 3.76 ( 1977) link_BETA1-4 : bond 0.00735 / 0.37 ( 2) link_BETA1-4 : angle 1.50383 / 0.93 ( 6) link_NAG-ASN : bond 0.00779 / 0.37 ( 25) link_NAG-ASN : angle 5.17172 / 3.16 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 82 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.6835 (m110) REVERT: A 229 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8631 (pt) REVERT: A 421 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: A 429 PHE cc_start: 0.8274 (t80) cc_final: 0.7831 (t80) REVERT: A 460 ASN cc_start: 0.8929 (p0) cc_final: 0.8449 (m-40) REVERT: A 587 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7566 (tp) REVERT: A 740 MET cc_start: 0.8420 (tmm) cc_final: 0.7700 (tmm) REVERT: A 802 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.7819 (p90) REVERT: A 851 CYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 69 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6391 (m-70) REVERT: B 215 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5200 (m-30) REVERT: B 468 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (mp) REVERT: B 740 MET cc_start: 0.9193 (tpt) cc_final: 0.8854 (tpp) REVERT: B 776 LYS cc_start: 0.9465 (tppp) cc_final: 0.9257 (tppt) REVERT: B 869 MET cc_start: 0.8219 (ptm) cc_final: 0.7879 (ptp) REVERT: B 985 ASP cc_start: 0.8227 (p0) cc_final: 0.7725 (p0) REVERT: B 988 GLU cc_start: 0.8656 (mp0) cc_final: 0.8450 (mp0) REVERT: B 1071 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8064 (tp40) REVERT: C 365 TYR cc_start: 0.9458 (m-80) cc_final: 0.9200 (m-80) REVERT: C 697 MET cc_start: 0.8741 (ttp) cc_final: 0.8280 (ttp) REVERT: C 775 ASP cc_start: 0.8593 (t0) cc_final: 0.8354 (t0) REVERT: C 921 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8265 (tptt) REVERT: L 78 LEU cc_start: 0.0306 (tp) cc_final: -0.0441 (mt) REVERT: L 97 PHE cc_start: 0.8369 (t80) cc_final: 0.7973 (t80) outliers start: 111 outliers final: 61 residues processed: 186 average time/residue: 0.1589 time to fit residues: 50.2787 Evaluate side-chains 142 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 70 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 88 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 333 optimal weight: 40.0000 chunk 230 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 115 GLN C 164 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.078725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.052051 restraints weight = 121764.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053938 restraints weight = 66223.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054447 restraints weight = 36844.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054701 restraints weight = 31184.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054723 restraints weight = 30769.713| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 26802 Z= 0.271 Angle : 0.851 20.981 36614 Z= 0.414 Chirality : 0.051 0.610 4308 Planarity : 0.006 0.074 4689 Dihedral : 7.252 57.847 3657 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.01 % Favored : 84.78 % Rotamer: Outliers : 3.98 % Allowed : 16.47 % Favored : 79.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.14), residues: 3317 helix: 0.69 (0.20), residues: 711 sheet: -2.53 (0.20), residues: 590 loop : -3.14 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.029 0.002 TYR A 707 PHE 0.025 0.002 PHE B 898 TRP 0.019 0.002 TRP B1102 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (26733) covalent geometry : angle 0.81870 / 0.41 (36449) SS BOND : bond 0.00514 / 0.24 ( 42) SS BOND : angle 1.92701 / 1.11 ( 84) hydrogen bonds : bond 0.04588 / 3.06 ( 707) hydrogen bonds : angle 5.90704 / 3.88 ( 1977) link_BETA1-4 : bond 0.01040 / 0.54 ( 2) link_BETA1-4 : angle 2.33409 / 1.44 ( 6) link_NAG-ASN : bond 0.00718 / 0.35 ( 25) link_NAG-ASN : angle 4.81555 / 2.95 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 75 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.6803 (m110) REVERT: A 229 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (pt) REVERT: A 378 LYS cc_start: 0.7951 (tptp) cc_final: 0.7707 (tptp) REVERT: A 421 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: A 429 PHE cc_start: 0.8580 (t80) cc_final: 0.7852 (t80) REVERT: A 460 ASN cc_start: 0.8980 (p0) cc_final: 0.8537 (m-40) REVERT: A 461 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6352 (pt) REVERT: A 562 PHE cc_start: 0.7265 (p90) cc_final: 0.6756 (p90) REVERT: A 587 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7678 (tp) REVERT: A 740 MET cc_start: 0.8528 (tmm) cc_final: 0.7904 (tmm) REVERT: A 851 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8294 (t) REVERT: B 69 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6520 (m-70) REVERT: B 215 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.5985 (m-30) REVERT: B 468 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 740 MET cc_start: 0.9267 (tpt) cc_final: 0.8935 (tpp) REVERT: B 1132 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8959 (pt) REVERT: C 387 LEU cc_start: 0.9174 (mm) cc_final: 0.8923 (mp) REVERT: C 389 ASP cc_start: 0.9005 (m-30) cc_final: 0.8637 (p0) REVERT: C 697 MET cc_start: 0.8768 (ttp) cc_final: 0.8315 (ttm) REVERT: C 775 ASP cc_start: 0.8743 (t0) cc_final: 0.8465 (t0) REVERT: C 921 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8368 (tptt) REVERT: C 1107 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7568 (tpm170) REVERT: L 78 LEU cc_start: 0.0895 (tp) cc_final: 0.0157 (mt) REVERT: L 97 PHE cc_start: 0.8351 (t80) cc_final: 0.7903 (t80) outliers start: 112 outliers final: 62 residues processed: 182 average time/residue: 0.1614 time to fit residues: 49.3751 Evaluate side-chains 138 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 64 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 99 optimal weight: 0.3980 chunk 157 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 224 optimal weight: 0.0670 chunk 234 optimal weight: 0.0570 chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 563 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN B 115 GLN B 920 GLN B1106 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.080875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053654 restraints weight = 120049.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.055463 restraints weight = 56615.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056591 restraints weight = 36224.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.057291 restraints weight = 27627.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.057710 restraints weight = 23421.262| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26802 Z= 0.127 Angle : 0.749 19.851 36614 Z= 0.359 Chirality : 0.049 0.586 4308 Planarity : 0.005 0.100 4689 Dihedral : 6.818 55.095 3646 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.28 % Favored : 88.54 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.14), residues: 3317 helix: 1.31 (0.21), residues: 685 sheet: -2.10 (0.21), residues: 583 loop : -2.97 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 357 TYR 0.023 0.001 TYR A 707 PHE 0.020 0.001 PHE A 559 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (26733) covalent geometry : angle 0.71545 / 0.35 (36449) SS BOND : bond 0.00455 / 0.23 ( 42) SS BOND : angle 1.69746 / 1.02 ( 84) hydrogen bonds : bond 0.03891 / 2.60 ( 707) hydrogen bonds : angle 5.42508 / 3.54 ( 1977) link_BETA1-4 : bond 0.00834 / 0.42 ( 2) link_BETA1-4 : angle 2.27584 / 1.45 ( 6) link_NAG-ASN : bond 0.00753 / 0.35 ( 25) link_NAG-ASN : angle 4.67087 / 2.82 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 80 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.6750 (m110) REVERT: A 229 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 231 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 378 LYS cc_start: 0.8006 (tptp) cc_final: 0.7655 (tptp) REVERT: A 421 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: A 429 PHE cc_start: 0.8497 (t80) cc_final: 0.7830 (t80) REVERT: A 562 PHE cc_start: 0.7227 (p90) cc_final: 0.6792 (p90) REVERT: A 740 MET cc_start: 0.8444 (tmm) cc_final: 0.7808 (tmm) REVERT: B 69 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6356 (m-70) REVERT: B 104 TRP cc_start: 0.6992 (OUTLIER) cc_final: 0.6062 (p-90) REVERT: B 215 ASP cc_start: 0.5885 (OUTLIER) cc_final: 0.5419 (m-30) REVERT: B 468 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 740 MET cc_start: 0.9142 (tpt) cc_final: 0.8916 (tpp) REVERT: B 1029 MET cc_start: 0.9456 (tpp) cc_final: 0.8964 (tpp) REVERT: C 697 MET cc_start: 0.8685 (ttp) cc_final: 0.8296 (ttm) REVERT: C 740 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8583 (tpp) REVERT: C 921 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8397 (tptt) REVERT: L 78 LEU cc_start: 0.0134 (tp) cc_final: -0.0816 (mt) REVERT: L 97 PHE cc_start: 0.8396 (t80) cc_final: 0.8003 (t80) outliers start: 84 outliers final: 53 residues processed: 156 average time/residue: 0.1631 time to fit residues: 42.8846 Evaluate side-chains 133 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 70 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 193 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 323 optimal weight: 50.0000 chunk 143 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 257 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.080771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053921 restraints weight = 119184.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.055663 restraints weight = 56339.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.056783 restraints weight = 35996.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057470 restraints weight = 27449.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.057840 restraints weight = 23179.854| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26802 Z= 0.126 Angle : 0.714 18.688 36614 Z= 0.341 Chirality : 0.048 0.561 4308 Planarity : 0.005 0.097 4689 Dihedral : 6.388 56.216 3638 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.00 % Favored : 87.82 % Rotamer: Outliers : 3.02 % Allowed : 17.99 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.14), residues: 3317 helix: 1.55 (0.21), residues: 680 sheet: -2.05 (0.21), residues: 591 loop : -2.81 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.030 0.001 TYR A 369 PHE 0.018 0.001 PHE B 490 TRP 0.018 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (26733) covalent geometry : angle 0.68421 / 0.33 (36449) SS BOND : bond 0.00396 / 0.19 ( 42) SS BOND : angle 1.31902 / 0.79 ( 84) hydrogen bonds : bond 0.03702 / 2.45 ( 707) hydrogen bonds : angle 5.25997 / 3.43 ( 1977) link_BETA1-4 : bond 0.00598 / 0.31 ( 2) link_BETA1-4 : angle 1.42153 / 0.88 ( 6) link_NAG-ASN : bond 0.00700 / 0.32 ( 25) link_NAG-ASN : angle 4.41623 / 2.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 81 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.6883 (m110) REVERT: A 229 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8697 (pt) REVERT: A 231 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (tp) REVERT: A 378 LYS cc_start: 0.8063 (tptp) cc_final: 0.7821 (tptp) REVERT: A 421 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: A 429 PHE cc_start: 0.8484 (t80) cc_final: 0.7778 (t80) REVERT: A 450 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8352 (p0) REVERT: A 740 MET cc_start: 0.8417 (tmm) cc_final: 0.7792 (tmm) REVERT: A 851 CYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (t) REVERT: A 1029 MET cc_start: 0.9448 (tpp) cc_final: 0.9238 (tpp) REVERT: B 69 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6417 (m-70) REVERT: B 104 TRP cc_start: 0.6763 (OUTLIER) cc_final: 0.5844 (p-90) REVERT: B 215 ASP cc_start: 0.6358 (OUTLIER) cc_final: 0.5955 (m-30) REVERT: B 380 TYR cc_start: 0.8278 (m-10) cc_final: 0.8023 (m-80) REVERT: B 574 ASP cc_start: 0.8476 (m-30) cc_final: 0.8198 (m-30) REVERT: B 1029 MET cc_start: 0.9464 (tpp) cc_final: 0.8922 (tpp) REVERT: B 1071 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8047 (tp40) REVERT: C 389 ASP cc_start: 0.9176 (m-30) cc_final: 0.8738 (p0) REVERT: C 488 CYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5464 (t) REVERT: C 697 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: C 900 MET cc_start: 0.8909 (mtp) cc_final: 0.8632 (mtt) REVERT: C 921 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8364 (tptt) REVERT: L 78 LEU cc_start: 0.0528 (tp) cc_final: -0.0362 (mm) outliers start: 85 outliers final: 53 residues processed: 160 average time/residue: 0.1662 time to fit residues: 44.9080 Evaluate side-chains 137 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 71 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 152 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 173 optimal weight: 0.0670 chunk 162 optimal weight: 5.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN C 334 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.078273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051113 restraints weight = 121315.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.052719 restraints weight = 59574.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053778 restraints weight = 38953.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.054433 restraints weight = 29981.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054831 restraints weight = 25574.262| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 26802 Z= 0.265 Angle : 0.805 18.747 36614 Z= 0.390 Chirality : 0.050 0.559 4308 Planarity : 0.005 0.089 4689 Dihedral : 6.570 54.164 3634 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.99 % Favored : 86.83 % Rotamer: Outliers : 2.99 % Allowed : 18.56 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.14), residues: 3317 helix: 1.06 (0.20), residues: 703 sheet: -2.21 (0.20), residues: 635 loop : -2.83 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 815 TYR 0.028 0.002 TYR A 369 PHE 0.026 0.002 PHE B 898 TRP 0.018 0.002 TRP B1102 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (26733) covalent geometry : angle 0.77866 / 0.38 (36449) SS BOND : bond 0.00400 / 0.21 ( 42) SS BOND : angle 1.27235 / 0.78 ( 84) hydrogen bonds : bond 0.04403 / 2.93 ( 707) hydrogen bonds : angle 5.60050 / 3.68 ( 1977) link_BETA1-4 : bond 0.00555 / 0.28 ( 2) link_BETA1-4 : angle 1.98607 / 1.20 ( 6) link_NAG-ASN : bond 0.00747 / 0.35 ( 25) link_NAG-ASN : angle 4.46644 / 2.71 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 73 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.6853 (m110) REVERT: A 229 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8720 (pt) REVERT: A 231 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (tp) REVERT: A 378 LYS cc_start: 0.8036 (tptp) cc_final: 0.7739 (tptp) REVERT: A 402 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7734 (pt) REVERT: A 429 PHE cc_start: 0.8574 (t80) cc_final: 0.7888 (t80) REVERT: A 450 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8227 (p0) REVERT: A 562 PHE cc_start: 0.7358 (p90) cc_final: 0.6876 (p90) REVERT: A 740 MET cc_start: 0.8489 (tmm) cc_final: 0.7841 (tmm) REVERT: A 851 CYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8292 (t) REVERT: B 69 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6306 (m-70) REVERT: B 104 TRP cc_start: 0.6817 (OUTLIER) cc_final: 0.5932 (p-90) REVERT: B 215 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: B 380 TYR cc_start: 0.8267 (m-10) cc_final: 0.8005 (m-80) REVERT: B 1071 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8050 (tp40) REVERT: C 389 ASP cc_start: 0.9209 (m-30) cc_final: 0.8764 (p0) REVERT: C 697 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8289 (ttm) REVERT: C 786 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8835 (pttm) REVERT: C 921 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (tptt) REVERT: C 1107 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7550 (tpm170) REVERT: L 20 THR cc_start: 0.5071 (t) cc_final: 0.4821 (m) REVERT: L 78 LEU cc_start: 0.0554 (tp) cc_final: -0.0267 (mm) outliers start: 84 outliers final: 58 residues processed: 149 average time/residue: 0.1744 time to fit residues: 42.9831 Evaluate side-chains 138 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 67 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1144 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 163 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 213 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.079720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052884 restraints weight = 120240.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.054585 restraints weight = 57636.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.055686 restraints weight = 37115.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056367 restraints weight = 28350.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056782 restraints weight = 24016.077| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26802 Z= 0.136 Angle : 0.715 18.433 36614 Z= 0.342 Chirality : 0.048 0.535 4308 Planarity : 0.005 0.083 4689 Dihedral : 6.383 55.906 3634 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.00 % Favored : 87.85 % Rotamer: Outliers : 3.02 % Allowed : 18.63 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.14), residues: 3317 helix: 1.40 (0.21), residues: 693 sheet: -2.06 (0.20), residues: 607 loop : -2.70 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.030 0.001 TYR A 369 PHE 0.028 0.001 PHE C 855 TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (26733) covalent geometry : angle 0.68794 / 0.34 (36449) SS BOND : bond 0.00347 / 0.18 ( 42) SS BOND : angle 1.12352 / 0.69 ( 84) hydrogen bonds : bond 0.03833 / 2.54 ( 707) hydrogen bonds : angle 5.31339 / 3.47 ( 1977) link_BETA1-4 : bond 0.00556 / 0.29 ( 2) link_BETA1-4 : angle 1.24685 / 0.75 ( 6) link_NAG-ASN : bond 0.00687 / 0.30 ( 25) link_NAG-ASN : angle 4.28748 / 2.58 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 71 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.6754 (m110) REVERT: A 187 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7226 (mmtt) REVERT: A 231 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 402 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7616 (pt) REVERT: A 429 PHE cc_start: 0.8461 (t80) cc_final: 0.7783 (t80) REVERT: A 562 PHE cc_start: 0.7348 (p90) cc_final: 0.6875 (p90) REVERT: A 740 MET cc_start: 0.8451 (tmm) cc_final: 0.7821 (tmm) REVERT: A 851 CYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8283 (t) REVERT: B 69 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6359 (m-70) REVERT: B 104 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.5896 (p-90) REVERT: B 1071 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: C 389 ASP cc_start: 0.9239 (m-30) cc_final: 0.8689 (p0) REVERT: C 488 CYS cc_start: 0.5380 (OUTLIER) cc_final: 0.5118 (t) REVERT: C 697 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8478 (ttm) REVERT: C 786 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8796 (pttm) REVERT: C 921 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8332 (tptp) REVERT: L 78 LEU cc_start: 0.0554 (tp) cc_final: -0.0359 (mm) outliers start: 85 outliers final: 54 residues processed: 148 average time/residue: 0.1703 time to fit residues: 42.5113 Evaluate side-chains 132 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 67 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 76 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 285 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.079439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.052595 restraints weight = 120579.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054290 restraints weight = 58185.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055383 restraints weight = 37567.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056065 restraints weight = 28698.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.056472 restraints weight = 24310.334| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26802 Z= 0.147 Angle : 0.715 18.416 36614 Z= 0.342 Chirality : 0.047 0.521 4308 Planarity : 0.005 0.080 4689 Dihedral : 6.235 59.332 3628 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.24 % Favored : 87.58 % Rotamer: Outliers : 2.45 % Allowed : 19.27 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 3317 helix: 1.43 (0.21), residues: 693 sheet: -2.06 (0.20), residues: 606 loop : -2.65 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1019 TYR 0.032 0.001 TYR A 369 PHE 0.029 0.001 PHE C 855 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (26733) covalent geometry : angle 0.68874 / 0.34 (36449) SS BOND : bond 0.00345 / 0.18 ( 42) SS BOND : angle 1.05856 / 0.65 ( 84) hydrogen bonds : bond 0.03832 / 2.53 ( 707) hydrogen bonds : angle 5.27406 / 3.45 ( 1977) link_BETA1-4 : bond 0.00728 / 0.37 ( 2) link_BETA1-4 : angle 1.38670 / 0.81 ( 6) link_NAG-ASN : bond 0.00670 / 0.30 ( 25) link_NAG-ASN : angle 4.20962 / 2.54 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 73 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.6751 (m110) REVERT: A 106 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8120 (p90) REVERT: A 187 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7225 (mmtt) REVERT: A 231 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 378 LYS cc_start: 0.8052 (tptp) cc_final: 0.7842 (tptp) REVERT: A 389 ASP cc_start: 0.8555 (m-30) cc_final: 0.8223 (m-30) REVERT: A 402 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7656 (pt) REVERT: A 429 PHE cc_start: 0.8463 (t80) cc_final: 0.7686 (t80) REVERT: A 562 PHE cc_start: 0.7342 (p90) cc_final: 0.6876 (p90) REVERT: A 740 MET cc_start: 0.8419 (tmm) cc_final: 0.7795 (tmm) REVERT: A 851 CYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8255 (t) REVERT: B 69 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6403 (m-70) REVERT: B 104 TRP cc_start: 0.6697 (OUTLIER) cc_final: 0.5863 (p-90) REVERT: B 1029 MET cc_start: 0.9451 (tpp) cc_final: 0.9079 (tpp) REVERT: B 1071 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: C 697 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: C 786 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8839 (pttm) REVERT: C 869 MET cc_start: 0.8735 (ptp) cc_final: 0.8281 (pmm) REVERT: C 921 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8354 (tptp) REVERT: C 1107 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7684 (tpm170) REVERT: L 78 LEU cc_start: 0.0821 (tp) cc_final: -0.0031 (mm) outliers start: 69 outliers final: 51 residues processed: 135 average time/residue: 0.1797 time to fit residues: 40.2107 Evaluate side-chains 131 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 68 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 333 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.078591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051388 restraints weight = 121751.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053094 restraints weight = 60195.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054149 restraints weight = 39417.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054791 restraints weight = 30377.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055196 restraints weight = 25979.009| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26802 Z= 0.207 Angle : 0.751 18.039 36614 Z= 0.361 Chirality : 0.048 0.505 4308 Planarity : 0.005 0.074 4689 Dihedral : 6.307 59.072 3628 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.57 % Favored : 87.25 % Rotamer: Outliers : 2.63 % Allowed : 19.20 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.14), residues: 3317 helix: 1.31 (0.21), residues: 693 sheet: -2.14 (0.20), residues: 648 loop : -2.69 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.030 0.002 TYR A 369 PHE 0.027 0.002 PHE C 855 TRP 0.015 0.002 TRP B 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (26733) covalent geometry : angle 0.72613 / 0.36 (36449) SS BOND : bond 0.00351 / 0.19 ( 42) SS BOND : angle 1.29924 / 0.82 ( 84) hydrogen bonds : bond 0.04070 / 2.70 ( 707) hydrogen bonds : angle 5.38651 / 3.53 ( 1977) link_BETA1-4 : bond 0.00454 / 0.24 ( 2) link_BETA1-4 : angle 1.34693 / 0.77 ( 6) link_NAG-ASN : bond 0.00690 / 0.31 ( 25) link_NAG-ASN : angle 4.16251 / 2.52 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6173.43 seconds wall clock time: 123 minutes 12.00 seconds (7392.00 seconds total)