Starting phenix.real_space_refine on Sun Jul 5 14:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.map" model { file = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q9m_13873/07_2026/7q9m_13873.cif" } resolution = 3.7 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= 0.001 sd= 0.014 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 125 5.16 5 C 18061 2.51 5 N 4676 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 28406 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7473 Classifications: {'peptide': 976} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 927} Chain breaks: 10 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 6, 'TYR:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 7596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7596 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 48, 'TRANS': 929} Chain breaks: 10 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7452 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 5, 'GLU:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "J" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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: "T" 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: "U" 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: "V" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.31, per 1000 atoms: 0.22 Number of scatterers: 28406 At special positions: 0 Unit cell: (131.2, 168.92, 205, 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 125 16.00 O 5544 8.00 N 4676 7.00 C 18061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 328 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A1071 " " NAG B1301 " - " ASN B 714 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 654 " " NAG C1303 " - " ASN C 706 " " NAG C1304 " - " ASN C1071 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN B 340 " " NAG P 1 " - " ASN B 798 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 340 " " NAG S 1 " - " ASN C1131 " " NAG T 1 " - " ASN C 714 " " NAG U 1 " - " ASN C 798 " " NAG V 1 " - " ASN C1095 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 58 sheets defined 22.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.334A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.089A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.636A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.522A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.602A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.541A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 3.790A pdb=" N ALA A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.442A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.129A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.272A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.150A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.523A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.522A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.134A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.269A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.981A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.013A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 753 removed outlier: 3.755A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 888 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.562A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 943 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.220A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.375A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.722A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.739A pdb=" N GLN J 65 " --> pdb=" O PRO J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.833A pdb=" N GLN E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.638A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 264 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 263 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 93 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.792A pdb=" N ASP A 53 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.505A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.138A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 610 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.600A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.579A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA8, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.233A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.669A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.569A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.294A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.481A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.126A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.281A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AC1, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.762A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC4, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.063A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.852A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.560A pdb=" N ILE B 711 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B1070 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.020A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.271A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.500A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.586A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.513A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.952A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.888A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.693A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.848A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.964A pdb=" N CYS C 522 " --> pdb=" O CYS C 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.550A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.601A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.601A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AE6, first strand: chain 'C' and resid 1117 through 1120 removed outlier: 3.730A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.667A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.539A pdb=" N HIS H 105 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.652A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.705A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.608A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.525A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.758A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.502A pdb=" N VAL F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.619A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3180 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: 7.52 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4979 1.33 - 1.45: 7984 1.45 - 1.57: 15921 1.57 - 1.69: 0 1.69 - 1.82: 158 Bond restraints: 29042 Sorted by residual: bond pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 bond pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.62e+00 bond pdb=" N SER L 28 " pdb=" CA SER L 28 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.88e+00 bond pdb=" N ALA L 25 " pdb=" CA ALA L 25 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" N SER L 26 " pdb=" CA SER L 26 " ideal model delta sigma weight residual 1.462 1.488 -0.027 1.26e-02 6.30e+03 4.42e+00 ... (remaining 29037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 37937 1.23 - 2.46: 1277 2.46 - 3.69: 287 3.69 - 4.92: 48 4.92 - 6.15: 8 Bond angle restraints: 39557 Sorted by residual: angle pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" O SER L 26 " ideal model delta sigma weight residual 120.92 116.29 4.63 1.04e+00 9.25e-01 1.99e+01 angle pdb=" CA SER L 28 " pdb=" C SER L 28 " pdb=" O SER L 28 " ideal model delta sigma weight residual 121.87 118.22 3.65 1.16e+00 7.43e-01 9.91e+00 angle pdb=" N SER B 755 " pdb=" CA SER B 755 " pdb=" CB SER B 755 " ideal model delta sigma weight residual 114.27 109.55 4.72 1.64e+00 3.72e-01 8.29e+00 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.96 110.12 2.84 1.00e+00 1.00e+00 8.08e+00 angle pdb=" N GLN L 27 " pdb=" CA GLN L 27 " pdb=" CB GLN L 27 " ideal model delta sigma weight residual 110.49 115.29 -4.80 1.69e+00 3.50e-01 8.07e+00 ... (remaining 39552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16188 17.94 - 35.89: 508 35.89 - 53.83: 109 53.83 - 71.77: 22 71.77 - 89.72: 10 Dihedral angle restraints: 16837 sinusoidal: 6377 harmonic: 10460 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -162.35 76.35 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -160.56 74.56 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 16834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4079 0.067 - 0.133: 524 0.133 - 0.200: 23 0.200 - 0.266: 1 0.266 - 0.333: 2 Chirality restraints: 4629 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.16e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 340 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4626 not shown) Planarity restraints: 5071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 994 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C ILE A 994 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE A 994 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 995 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 523 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 524 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 230 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.017 5.00e-02 4.00e+02 ... (remaining 5068 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 202 2.53 - 3.12: 22721 3.12 - 3.71: 42646 3.71 - 4.31: 61782 4.31 - 4.90: 103878 Nonbonded interactions: 231229 Sorted by model distance: nonbonded pdb=" O LYS F 108 " pdb=" CG ARG F 109 " model vdw 1.937 3.440 nonbonded pdb=" O PHE B 559 " pdb=" NZ LYS C 41 " model vdw 2.046 3.120 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR C 615 " pdb=" OE1 GLU C 616 " model vdw 2.071 3.040 nonbonded pdb=" OG SER E 31 " pdb=" OD2 ASP E 52 " model vdw 2.074 3.040 ... (remaining 231224 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 87 or resid 90 through 96 or resid 100 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or re \ sid 141 through 240 or resid 261 through 328 or (resid 329 and (name N or name C \ A or name C or name O or name CB )) or resid 330 through 370 or (resid 371 and ( \ name N or name CA or name C or name O or name CB )) or resid 372 through 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 \ through 382 or (resid 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 through 452 or (resid 453 through 456 and (name N or name CA or \ name C or name O or name CB )) or resid 457 through 458 or (resid 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 461 or (res \ id 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) \ or resid 503 through 525 or (resid 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 532 or (resid 533 through 534 and (name N o \ r name CA or name C or name O or name CB )) or resid 535 through 549 or (resid 5 \ 50 through 551 and (name N or name CA or name C or name O or name CB )) or resid \ 552 through 553 or (resid 554 through 555 and (name N or name CA or name C or n \ ame O or name CB )) or resid 556 or (resid 557 and (name N or name CA or name C \ or name O or name CB )) or resid 558 or (resid 559 and (name N or name CA or nam \ e C or name O or name CB )) or resid 560 through 570 or (resid 571 through 572 a \ nd (name N or name CA or name C or name O or name CB )) or resid 573 or (resid 5 \ 74 through 575 and (name N or name CA or name C or name O or name CB )) or resid \ 576 through 580 or (resid 581 and (name N or name CA or name C or name O or nam \ e CB )) or resid 582 through 672 or (resid 687 and (name N or name CA or name C \ or name O or name CB )) or resid 688 through 782 or (resid 783 and (name N or na \ me CA or name C or name O or name CB )) or resid 784 through 792 or (resid 793 a \ nd (name N or name CA or name C or name O or name CB )) or resid 794 through 821 \ or (resid 822 and (name N or name CA or name C or name O or name CB )) or resid \ 823 through 824 or resid 852 through 929 or (resid 930 and (name N or name CA o \ r name C or name O or name CB )) or resid 931 through 936 or resid 942 through 9 \ 79 or (resid 980 and (name N or name CA or name C or name O or name CB )) or res \ id 981 through 991 or (resid 992 and (name N or name CA or name C or name O or n \ ame CB )) or resid 993 through 1103 or (resid 1104 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1105 through 1304)) selection = (chain 'B' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 65 or re \ sid 82 through 87 or resid 90 through 95 or (resid 96 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 101 or (resid 102 and (name \ N or name CA or name C or name O or name CB )) or resid 103 through 121 or resid \ 126 through 128 or (resid 129 and (name N or name CA or name C or name O or nam \ e CB )) or resid 130 through 139 or (resid 140 and (name N or name CA or name C \ or name O or name CB )) or resid 141 through 171 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 or (resid 202 through 203 and (name N or name CA or name C or name O or nam \ e CB )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 232 or (resid 233 and (name N or na \ me CA or name C or name O )) or resid 234 or (resid 235 and (name N or name CA o \ r name C or name O or name CB )) or resid 236 through 277 or (resid 278 and (nam \ e N or name CA or name C or name O or name CB )) or resid 279 through 336 or (re \ sid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 th \ rough 342 or (resid 343 and (name N or name CA or name C or name O or name CB )) \ or resid 344 through 365 or (resid 366 and (name N or name CA or name C or name \ O or name CB )) or resid 367 through 370 or (resid 371 and (name N or name CA o \ r name C or name O or name CB )) or resid 372 through 373 or (resid 374 through \ 375 and (name N or name CA or name C or name O or name CB )) or resid 376 throug \ h 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or \ resid 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or (resid 389 and (name N or name CA or name C or name O or name CB )) or resid \ 390 through 452 or (resid 453 through 456 and (name N or name CA or name C or n \ ame O or name CB )) or resid 457 through 458 or (resid 459 and (name N or name C \ A or name C or name O or name CB )) or resid 460 through 461 or (resid 462 and ( \ name N or name CA or name C or name O or name CB )) or resid 463 through 470 or \ (resid 471 through 472 and (name N or name CA or name C or name O or name CB )) \ or resid 473 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 497 or (resid 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 501 or (resid 502 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 525 or (res \ id 526 and (name N or name CA or name C or name O or name CB )) or resid 527 thr \ ough 532 or (resid 533 through 534 and (name N or name CA or name C or name O or \ name CB )) or resid 535 through 549 or (resid 550 through 551 and (name N or na \ me CA or name C or name O or name CB )) or resid 552 through 553 or (resid 554 t \ hrough 555 and (name N or name CA or name C or name O or name CB )) or resid 556 \ or (resid 557 and (name N or name CA or name C or name O or name CB )) or resid \ 558 or (resid 559 and (name N or name CA or name C or name O or name CB )) or r \ esid 560 through 570 or (resid 571 through 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 or (resid 574 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 671 or (resid 672 a \ nd (name N or name CA or name C or name O or name CB )) or resid 687 through 821 \ or (resid 822 and (name N or name CA or name C or name O or name CB )) or resid \ 823 through 824 or resid 852 through 929 or (resid 930 and (name N or name CA o \ r name C or name O or name CB )) or resid 931 through 936 or resid 942 through 9 \ 79 or (resid 980 and (name N or name CA or name C or name O or name CB )) or res \ id 981 or (resid 982 and (name N or name CA or name C or name O or name CB )) or \ resid 983 through 984 or (resid 985 through 987 and (name N or name CA or name \ C or name O or name CB )) or resid 988 through 991 or (resid 992 and (name N or \ name CA or name C or name O or name CB )) or resid 993 through 1141 or (resid 11 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 1143 throug \ h 1304)) selection = (chain 'C' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 65 or re \ sid 82 through 95 or (resid 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 100 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 171 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 or (resid 202 through 203 and (name N or name CA or name C or name O or nam \ e CB )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 225 or (resid 226 and (name N or na \ me CA or name C or name O or name CB )) or resid 227 through 232 or (resid 233 a \ nd (name N or name CA or name C or name O )) or resid 234 or (resid 235 and (nam \ e N or name CA or name C or name O or name CB )) or resid 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )) or resid 238 through 240 or \ resid 261 through 328 or (resid 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 384 or (resid 385 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 389 and (name N or name CA or name C or \ name O or name CB )) or resid 390 through 497 or (resid 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 513 or resid 521 throu \ gh 574 or (resid 575 and (name N or name CA or name C or name O or name CB )) or \ resid 576 through 579 or (resid 580 through 581 and (name N or name CA or name \ C or name O or name CB )) or resid 582 through 782 or (resid 783 and (name N or \ name CA or name C or name O or name CB )) or resid 784 through 792 or (resid 793 \ and (name N or name CA or name C or name O or name CB )) or resid 794 through 9 \ 81 or (resid 982 and (name N or name CA or name C or name O or name CB )) or res \ id 983 through 984 or (resid 985 through 987 and (name N or name CA or name C or \ name O or name CB )) or resid 988 through 1103 or (resid 1104 and (name N or na \ me CA or name C or name O or name CB )) or resid 1105 through 1141 or (resid 114 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1143 through \ 1304)) } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = (chain 'E' and (resid 2 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 120)) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.730 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29128 Z= 0.199 Angle : 0.572 6.149 39772 Z= 0.310 Chirality : 0.044 0.333 4629 Planarity : 0.003 0.031 5043 Dihedral : 9.559 89.717 9986 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.95 % Favored : 96.91 % Rotamer: Outliers : 0.75 % Allowed : 2.78 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.25 (0.14), residues: 3531 helix: 2.11 (0.20), residues: 666 sheet: -0.01 (0.17), residues: 918 loop : -0.39 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 325 TYR 0.017 0.001 TYR A1064 PHE 0.012 0.001 PHE B 799 TRP 0.007 0.001 TRP C1099 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (29042) covalent geometry : angle 0.56457 / 0.31 (39557) SS BOND : bond 0.00253 / 0.17 ( 43) SS BOND : angle 0.63801 / 0.43 ( 86) hydrogen bonds : bond 0.13459 / 8.69 ( 1168) hydrogen bonds : angle 7.02438 / 4.80 ( 3180) link_BETA1-4 : bond 0.00268 / 0.17 ( 15) link_BETA1-4 : angle 1.39448 / 0.96 ( 45) link_NAG-ASN : bond 0.00328 / 0.21 ( 28) link_NAG-ASN : angle 1.76501 / 1.09 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 550 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8747 (pm20) cc_final: 0.8478 (pm20) REVERT: A 272 PHE cc_start: 0.8781 (m-80) cc_final: 0.8067 (m-10) REVERT: A 393 TYR cc_start: 0.8849 (m-80) cc_final: 0.8436 (m-10) REVERT: A 579 LEU cc_start: 0.8648 (mt) cc_final: 0.8383 (pt) REVERT: A 866 MET cc_start: 0.8456 (mtt) cc_final: 0.8124 (mtt) REVERT: B 129 LYS cc_start: 0.8252 (mttt) cc_final: 0.7780 (mmmt) REVERT: B 202 LYS cc_start: 0.8716 (mttm) cc_final: 0.8514 (mmmm) REVERT: B 284 ASP cc_start: 0.8452 (t0) cc_final: 0.8248 (t0) REVERT: B 335 PHE cc_start: 0.8197 (m-80) cc_final: 0.7556 (m-80) REVERT: B 433 TRP cc_start: 0.7228 (p90) cc_final: 0.6962 (p90) REVERT: B 855 LEU cc_start: 0.8121 (mp) cc_final: 0.7839 (mp) REVERT: B 1026 MET cc_start: 0.9062 (tpp) cc_final: 0.8844 (tpp) REVERT: C 32 PHE cc_start: 0.8992 (m-80) cc_final: 0.8712 (m-10) REVERT: C 262 TYR cc_start: 0.6519 (p90) cc_final: 0.6209 (p90) REVERT: C 399 ILE cc_start: 0.7940 (pt) cc_final: 0.7601 (pt) REVERT: C 433 TRP cc_start: 0.8189 (p90) cc_final: 0.7715 (p90) REVERT: C 537 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7380 (m-40) REVERT: C 581 ILE cc_start: 0.8531 (mm) cc_final: 0.7883 (mm) REVERT: C 1001 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9341 (tt) REVERT: H 34 ILE cc_start: 0.8134 (tt) cc_final: 0.7857 (tp) REVERT: H 80 TYR cc_start: 0.8969 (m-80) cc_final: 0.8660 (m-80) REVERT: L 36 TYR cc_start: 0.7286 (m-80) cc_final: 0.7000 (m-80) REVERT: L 49 TYR cc_start: 0.7994 (p90) cc_final: 0.7784 (p90) REVERT: J 98 ARG cc_start: 0.8191 (ttm170) cc_final: 0.6944 (ttm170) REVERT: K 4 MET cc_start: 0.9117 (mmm) cc_final: 0.8701 (mmm) REVERT: K 54 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7628 (tmm-80) REVERT: E 95 TYR cc_start: 0.7237 (m-80) cc_final: 0.6760 (m-80) outliers start: 23 outliers final: 4 residues processed: 568 average time/residue: 0.2012 time to fit residues: 180.1134 Evaluate side-chains 316 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 310 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain E residue 33 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 52 GLN C 447 ASN C 652 HIS C 911 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094162 restraints weight = 70197.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093132 restraints weight = 44352.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093279 restraints weight = 32757.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093520 restraints weight = 29982.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093798 restraints weight = 25561.169| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29128 Z= 0.139 Angle : 0.608 9.640 39772 Z= 0.308 Chirality : 0.045 0.243 4629 Planarity : 0.004 0.052 5043 Dihedral : 4.327 51.907 3862 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 1.80 % Allowed : 8.87 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.45 (0.14), residues: 3531 helix: 2.33 (0.20), residues: 670 sheet: 0.21 (0.17), residues: 858 loop : -0.33 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.033 0.002 TYR H 60 PHE 0.021 0.002 PHE B 194 TRP 0.036 0.002 TRP B 104 HIS 0.008 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (29042) covalent geometry : angle 0.59965 / 0.31 (39557) SS BOND : bond 0.00317 / 0.24 ( 43) SS BOND : angle 1.31934 / 0.79 ( 86) hydrogen bonds : bond 0.03854 / 2.47 ( 1168) hydrogen bonds : angle 5.68262 / 3.86 ( 3180) link_BETA1-4 : bond 0.00357 / 0.19 ( 15) link_BETA1-4 : angle 1.16330 / 0.84 ( 45) link_NAG-ASN : bond 0.00220 / 0.14 ( 28) link_NAG-ASN : angle 1.76059 / 1.14 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 370 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7930 (m-90) cc_final: 0.7550 (m-90) REVERT: A 224 GLU cc_start: 0.8702 (pm20) cc_final: 0.8404 (pm20) REVERT: A 266 TYR cc_start: 0.7919 (m-80) cc_final: 0.7697 (m-80) REVERT: A 272 PHE cc_start: 0.8677 (m-80) cc_final: 0.8229 (m-10) REVERT: A 335 PHE cc_start: 0.9085 (m-10) cc_final: 0.8859 (m-10) REVERT: A 393 TYR cc_start: 0.8815 (m-80) cc_final: 0.8372 (m-10) REVERT: A 494 PHE cc_start: 0.7858 (m-80) cc_final: 0.7434 (m-80) REVERT: A 652 HIS cc_start: 0.7958 (t70) cc_final: 0.7716 (t70) REVERT: A 728 MET cc_start: 0.8398 (ptm) cc_final: 0.7887 (ptm) REVERT: A 866 MET cc_start: 0.8433 (mtt) cc_final: 0.8095 (mtt) REVERT: B 129 LYS cc_start: 0.8267 (mttt) cc_final: 0.7888 (mmmt) REVERT: B 202 LYS cc_start: 0.8777 (mttm) cc_final: 0.8389 (mmmm) REVERT: B 295 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: B 335 PHE cc_start: 0.7973 (m-80) cc_final: 0.7692 (m-80) REVERT: B 433 TRP cc_start: 0.7138 (p90) cc_final: 0.6785 (p90) REVERT: B 803 LEU cc_start: 0.8974 (mt) cc_final: 0.8712 (mm) REVERT: B 855 LEU cc_start: 0.8352 (mp) cc_final: 0.7979 (mp) REVERT: B 952 ASN cc_start: 0.8191 (m-40) cc_final: 0.7925 (t0) REVERT: B 980 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7972 (mtm-85) REVERT: B 987 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: B 1080 HIS cc_start: 0.7793 (t70) cc_final: 0.7530 (t70) REVERT: C 262 TYR cc_start: 0.6537 (p90) cc_final: 0.6125 (p90) REVERT: C 266 TYR cc_start: 0.7387 (m-80) cc_final: 0.7061 (m-80) REVERT: C 367 ASN cc_start: 0.8584 (m-40) cc_final: 0.8219 (p0) REVERT: C 397 PHE cc_start: 0.8104 (p90) cc_final: 0.7757 (p90) REVERT: C 399 ILE cc_start: 0.7919 (pt) cc_final: 0.7559 (pt) REVERT: C 433 TRP cc_start: 0.8285 (p90) cc_final: 0.7840 (p90) REVERT: C 581 ILE cc_start: 0.8398 (mm) cc_final: 0.7781 (mm) REVERT: C 737 MET cc_start: 0.7590 (mtp) cc_final: 0.7330 (mtp) REVERT: C 801 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: C 892 GLN cc_start: 0.8480 (pm20) cc_final: 0.8261 (pm20) REVERT: C 1001 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9339 (tt) REVERT: L 49 TYR cc_start: 0.8127 (p90) cc_final: 0.7763 (p90) REVERT: K 4 MET cc_start: 0.8982 (mmm) cc_final: 0.8705 (mmm) REVERT: K 54 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7739 (tmm-80) REVERT: E 95 TYR cc_start: 0.7443 (m-80) cc_final: 0.7214 (m-80) REVERT: F 4 MET cc_start: 0.5868 (mtp) cc_final: 0.5420 (mtp) REVERT: F 38 GLN cc_start: 0.9484 (tt0) cc_final: 0.9233 (tp-100) REVERT: F 46 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 55 outliers final: 26 residues processed: 401 average time/residue: 0.2052 time to fit residues: 128.8559 Evaluate side-chains 318 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 801 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 264 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 341 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 277 optimal weight: 3.9990 chunk 350 optimal weight: 30.0000 chunk 188 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A 962 GLN A1116 ASN ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN B 932 GLN C 898 GLN C 916 ASN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 HIS H 59 ASN L 42 GLN L 89 GLN K 27 GLN E 27 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.150483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093256 restraints weight = 70246.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093795 restraints weight = 45100.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092973 restraints weight = 31885.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093399 restraints weight = 31986.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094037 restraints weight = 26468.294| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29128 Z= 0.206 Angle : 0.605 10.619 39772 Z= 0.307 Chirality : 0.045 0.245 4629 Planarity : 0.004 0.060 5043 Dihedral : 4.456 50.752 3860 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 2.29 % Allowed : 10.18 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.27 (0.14), residues: 3531 helix: 2.12 (0.20), residues: 673 sheet: 0.15 (0.17), residues: 893 loop : -0.47 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 45 TYR 0.020 0.002 TYR H 60 PHE 0.018 0.002 PHE A 92 TRP 0.030 0.002 TRP B 104 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (29042) covalent geometry : angle 0.59449 / 0.30 (39557) SS BOND : bond 0.00361 / 0.26 ( 43) SS BOND : angle 1.77095 / 1.06 ( 86) hydrogen bonds : bond 0.03816 / 2.44 ( 1168) hydrogen bonds : angle 5.57165 / 3.79 ( 3180) link_BETA1-4 : bond 0.00254 / 0.15 ( 15) link_BETA1-4 : angle 1.22118 / 0.87 ( 45) link_NAG-ASN : bond 0.00282 / 0.18 ( 28) link_NAG-ASN : angle 1.73548 / 1.10 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 309 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7979 (m-90) cc_final: 0.7472 (m-90) REVERT: A 224 GLU cc_start: 0.8802 (pm20) cc_final: 0.8530 (pm20) REVERT: A 266 TYR cc_start: 0.8007 (m-80) cc_final: 0.7806 (m-80) REVERT: A 272 PHE cc_start: 0.8627 (m-80) cc_final: 0.8279 (m-10) REVERT: A 335 PHE cc_start: 0.9124 (m-10) cc_final: 0.8892 (m-10) REVERT: A 393 TYR cc_start: 0.9098 (m-80) cc_final: 0.8619 (m-10) REVERT: A 449 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9266 (tt) REVERT: A 494 PHE cc_start: 0.7934 (m-80) cc_final: 0.7520 (m-80) REVERT: A 866 MET cc_start: 0.8503 (mtt) cc_final: 0.8193 (mtt) REVERT: A 915 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 952 ASN cc_start: 0.8096 (t0) cc_final: 0.7647 (t0) REVERT: A 1094 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9152 (p) REVERT: B 53 ASP cc_start: 0.7564 (t70) cc_final: 0.7258 (t70) REVERT: B 104 TRP cc_start: 0.6594 (m-90) cc_final: 0.6284 (m-90) REVERT: B 202 LYS cc_start: 0.8768 (mttm) cc_final: 0.8402 (mmmm) REVERT: B 295 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: B 335 PHE cc_start: 0.8130 (m-80) cc_final: 0.7782 (m-80) REVERT: B 348 TYR cc_start: 0.9280 (p90) cc_final: 0.9075 (p90) REVERT: B 433 TRP cc_start: 0.7354 (p90) cc_final: 0.6889 (p90) REVERT: B 855 LEU cc_start: 0.8479 (mp) cc_final: 0.8078 (mp) REVERT: B 866 MET cc_start: 0.8166 (mtm) cc_final: 0.7800 (ttm) REVERT: B 987 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: B 1026 MET cc_start: 0.8791 (tpp) cc_final: 0.8014 (ttm) REVERT: C 206 LYS cc_start: 0.8707 (tptt) cc_final: 0.8434 (tptt) REVERT: C 367 ASN cc_start: 0.8731 (m-40) cc_final: 0.8375 (p0) REVERT: C 399 ILE cc_start: 0.7777 (pt) cc_final: 0.7471 (pt) REVERT: C 405 ARG cc_start: 0.8308 (ppt170) cc_final: 0.7890 (ppt170) REVERT: C 433 TRP cc_start: 0.8348 (p90) cc_final: 0.7807 (p90) REVERT: C 581 ILE cc_start: 0.8458 (mm) cc_final: 0.7850 (mm) REVERT: C 855 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8908 (mt) REVERT: C 1001 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9298 (tt) REVERT: H 80 TYR cc_start: 0.9338 (m-80) cc_final: 0.8703 (m-80) REVERT: L 45 ARG cc_start: 0.8881 (mmm160) cc_final: 0.8659 (mmm160) REVERT: L 49 TYR cc_start: 0.8199 (p90) cc_final: 0.7828 (p90) REVERT: L 89 GLN cc_start: 0.3524 (OUTLIER) cc_final: 0.2877 (tp40) REVERT: J 48 MET cc_start: 0.8549 (mpp) cc_final: 0.8261 (mpp) REVERT: J 80 TYR cc_start: 0.8992 (m-80) cc_final: 0.8627 (t80) REVERT: K 54 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7991 (ttp-170) REVERT: E 95 TYR cc_start: 0.7673 (m-80) cc_final: 0.7378 (m-80) REVERT: F 4 MET cc_start: 0.6474 (mtp) cc_final: 0.6079 (mtp) REVERT: F 38 GLN cc_start: 0.9567 (tt0) cc_final: 0.9337 (tp-100) outliers start: 70 outliers final: 43 residues processed: 354 average time/residue: 0.1781 time to fit residues: 100.2622 Evaluate side-chains 329 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 339 optimal weight: 0.0000 chunk 173 optimal weight: 0.7980 chunk 310 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 330 optimal weight: 9.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1116 ASN B 385 ASN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** F 37 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 = 0.4249 r_free = 0.4249 target = 0.151126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091881 restraints weight = 69734.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093696 restraints weight = 43465.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094599 restraints weight = 26754.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095198 restraints weight = 20109.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095514 restraints weight = 19344.793| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29128 Z= 0.119 Angle : 0.554 12.098 39772 Z= 0.279 Chirality : 0.043 0.215 4629 Planarity : 0.004 0.061 5043 Dihedral : 4.315 50.236 3860 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.96 % Allowed : 11.52 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.39 (0.14), residues: 3531 helix: 2.36 (0.20), residues: 667 sheet: 0.12 (0.17), residues: 910 loop : -0.38 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 980 TYR 0.048 0.001 TYR H 60 PHE 0.032 0.001 PHE F 71 TRP 0.021 0.001 TRP C 350 HIS 0.008 0.001 HIS H 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29042) covalent geometry : angle 0.54761 / 0.28 (39557) SS BOND : bond 0.00237 / 0.17 ( 43) SS BOND : angle 0.90843 / 0.53 ( 86) hydrogen bonds : bond 0.03400 / 2.18 ( 1168) hydrogen bonds : angle 5.29933 / 3.60 ( 3180) link_BETA1-4 : bond 0.00310 / 0.17 ( 15) link_BETA1-4 : angle 1.10435 / 0.78 ( 45) link_NAG-ASN : bond 0.00209 / 0.12 ( 28) link_NAG-ASN : angle 1.56026 / 0.99 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7903 (m-90) cc_final: 0.7418 (m-90) REVERT: A 135 PHE cc_start: 0.6335 (p90) cc_final: 0.6128 (p90) REVERT: A 224 GLU cc_start: 0.8778 (pm20) cc_final: 0.8458 (pm20) REVERT: A 266 TYR cc_start: 0.7902 (m-80) cc_final: 0.7639 (m-10) REVERT: A 272 PHE cc_start: 0.8502 (m-80) cc_final: 0.8235 (m-10) REVERT: A 335 PHE cc_start: 0.9183 (m-10) cc_final: 0.8870 (m-80) REVERT: A 393 TYR cc_start: 0.9032 (m-80) cc_final: 0.8603 (m-80) REVERT: A 449 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9284 (tt) REVERT: A 866 MET cc_start: 0.8427 (mtt) cc_final: 0.8119 (mtt) REVERT: A 915 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 952 ASN cc_start: 0.8020 (t0) cc_final: 0.7557 (t0) REVERT: B 129 LYS cc_start: 0.8360 (mttt) cc_final: 0.8138 (mmmt) REVERT: B 202 LYS cc_start: 0.8781 (mttm) cc_final: 0.8420 (mmmm) REVERT: B 271 THR cc_start: 0.9057 (m) cc_final: 0.8425 (p) REVERT: B 295 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 335 PHE cc_start: 0.8028 (m-80) cc_final: 0.7695 (m-80) REVERT: B 348 TYR cc_start: 0.9227 (p90) cc_final: 0.9023 (p90) REVERT: B 352 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8354 (ttt180) REVERT: B 433 TRP cc_start: 0.7263 (p90) cc_final: 0.6799 (p90) REVERT: B 855 LEU cc_start: 0.8395 (mp) cc_final: 0.7979 (mp) REVERT: B 866 MET cc_start: 0.8162 (mtm) cc_final: 0.7715 (ttm) REVERT: B 987 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: B 1026 MET cc_start: 0.8783 (tpp) cc_final: 0.7939 (ttm) REVERT: B 1031 LEU cc_start: 0.9180 (mt) cc_final: 0.8643 (mp) REVERT: C 266 TYR cc_start: 0.7575 (m-80) cc_final: 0.7221 (m-80) REVERT: C 350 TRP cc_start: 0.7942 (p-90) cc_final: 0.7609 (p-90) REVERT: C 367 ASN cc_start: 0.8767 (m-40) cc_final: 0.8453 (p0) REVERT: C 399 ILE cc_start: 0.7909 (pt) cc_final: 0.7479 (pt) REVERT: C 405 ARG cc_start: 0.8366 (ppt170) cc_final: 0.7853 (ppt170) REVERT: C 492 TYR cc_start: 0.5391 (m-80) cc_final: 0.5106 (m-80) REVERT: C 581 ILE cc_start: 0.8380 (mm) cc_final: 0.7785 (mm) REVERT: C 728 MET cc_start: 0.9171 (ptp) cc_final: 0.8946 (ptp) REVERT: C 855 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8801 (mt) REVERT: C 1001 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9283 (tt) REVERT: C 1026 MET cc_start: 0.8932 (tpp) cc_final: 0.8334 (ttm) REVERT: H 46 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8197 (tm-30) REVERT: H 80 TYR cc_start: 0.9267 (m-80) cc_final: 0.8604 (m-80) REVERT: L 49 TYR cc_start: 0.8123 (p90) cc_final: 0.7693 (p90) REVERT: J 48 MET cc_start: 0.8520 (mpp) cc_final: 0.8296 (mpp) REVERT: J 106 LEU cc_start: 0.8858 (mt) cc_final: 0.8432 (tp) REVERT: K 54 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8022 (ttp-170) REVERT: E 95 TYR cc_start: 0.7609 (m-80) cc_final: 0.7346 (m-80) REVERT: F 4 MET cc_start: 0.6486 (mtp) cc_final: 0.5975 (mtp) outliers start: 60 outliers final: 34 residues processed: 346 average time/residue: 0.1907 time to fit residues: 105.6040 Evaluate side-chains 323 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 343 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 67 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.150526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093164 restraints weight = 70076.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093013 restraints weight = 47179.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093320 restraints weight = 30076.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093921 restraints weight = 27389.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094136 restraints weight = 24446.578| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 29128 Z= 0.169 Angle : 0.571 10.066 39772 Z= 0.288 Chirality : 0.044 0.210 4629 Planarity : 0.004 0.052 5043 Dihedral : 4.367 49.862 3859 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.29 % Allowed : 11.69 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.34 (0.14), residues: 3531 helix: 2.34 (0.20), residues: 658 sheet: 0.20 (0.17), residues: 874 loop : -0.46 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.022 0.001 TYR H 60 PHE 0.029 0.001 PHE F 71 TRP 0.029 0.001 TRP B 104 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (29042) covalent geometry : angle 0.56143 / 0.29 (39557) SS BOND : bond 0.00410 / 0.31 ( 43) SS BOND : angle 1.72128 / 0.93 ( 86) hydrogen bonds : bond 0.03546 / 2.31 ( 1168) hydrogen bonds : angle 5.27756 / 3.58 ( 3180) link_BETA1-4 : bond 0.00249 / 0.14 ( 15) link_BETA1-4 : angle 1.08491 / 0.75 ( 45) link_NAG-ASN : bond 0.00253 / 0.15 ( 28) link_NAG-ASN : angle 1.49990 / 0.94 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7949 (m-90) cc_final: 0.7505 (m-90) REVERT: A 135 PHE cc_start: 0.6355 (p90) cc_final: 0.6087 (p90) REVERT: A 224 GLU cc_start: 0.8824 (pm20) cc_final: 0.8594 (pm20) REVERT: A 266 TYR cc_start: 0.7983 (m-80) cc_final: 0.7564 (m-10) REVERT: A 272 PHE cc_start: 0.8549 (m-80) cc_final: 0.8317 (m-10) REVERT: A 323 ILE cc_start: 0.6865 (mt) cc_final: 0.6485 (tt) REVERT: A 335 PHE cc_start: 0.9155 (m-10) cc_final: 0.8826 (m-80) REVERT: A 393 TYR cc_start: 0.8878 (m-80) cc_final: 0.8527 (m-80) REVERT: A 449 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9271 (tt) REVERT: A 494 PHE cc_start: 0.8533 (m-80) cc_final: 0.7974 (m-80) REVERT: A 866 MET cc_start: 0.8473 (mtt) cc_final: 0.8166 (mtt) REVERT: A 915 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 952 ASN cc_start: 0.8164 (t0) cc_final: 0.7630 (t0) REVERT: B 104 TRP cc_start: 0.6857 (m-90) cc_final: 0.6258 (m-90) REVERT: B 202 LYS cc_start: 0.8794 (mttm) cc_final: 0.8439 (mmmm) REVERT: B 271 THR cc_start: 0.9041 (m) cc_final: 0.8438 (p) REVERT: B 295 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 352 ARG cc_start: 0.8711 (ttm170) cc_final: 0.8270 (ttt180) REVERT: B 433 TRP cc_start: 0.7289 (p90) cc_final: 0.6813 (p90) REVERT: B 855 LEU cc_start: 0.8297 (mp) cc_final: 0.7932 (mt) REVERT: B 866 MET cc_start: 0.8151 (mtm) cc_final: 0.7727 (ttm) REVERT: B 1031 LEU cc_start: 0.9196 (mt) cc_final: 0.8675 (mp) REVERT: C 206 LYS cc_start: 0.8861 (tptt) cc_final: 0.8611 (tptt) REVERT: C 350 TRP cc_start: 0.8116 (p-90) cc_final: 0.7889 (p-90) REVERT: C 389 PHE cc_start: 0.8133 (m-80) cc_final: 0.7857 (m-80) REVERT: C 399 ILE cc_start: 0.8107 (pt) cc_final: 0.7384 (pt) REVERT: C 405 ARG cc_start: 0.8425 (ppt170) cc_final: 0.7893 (ppt170) REVERT: C 433 TRP cc_start: 0.8239 (p90) cc_final: 0.8036 (p90) REVERT: C 581 ILE cc_start: 0.8455 (mm) cc_final: 0.7848 (mm) REVERT: C 728 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8878 (ptp) REVERT: C 855 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 1001 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9297 (tt) REVERT: H 80 TYR cc_start: 0.9143 (m-80) cc_final: 0.8486 (m-80) REVERT: L 45 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8471 (mmm160) REVERT: L 49 TYR cc_start: 0.7986 (p90) cc_final: 0.7632 (p90) REVERT: J 4 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8689 (mp) REVERT: J 80 TYR cc_start: 0.8806 (m-80) cc_final: 0.8383 (t80) REVERT: K 24 ARG cc_start: 0.9165 (mtm-85) cc_final: 0.8751 (mpp-170) REVERT: K 54 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8042 (ttp-170) REVERT: E 95 TYR cc_start: 0.7445 (m-80) cc_final: 0.7210 (m-80) REVERT: F 4 MET cc_start: 0.6193 (mtp) cc_final: 0.5775 (mtp) outliers start: 70 outliers final: 46 residues processed: 343 average time/residue: 0.1965 time to fit residues: 107.5736 Evaluate side-chains 329 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 352 optimal weight: 50.0000 chunk 137 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 308 optimal weight: 40.0000 chunk 338 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 74 optimal weight: 0.6980 chunk 300 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.150193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093502 restraints weight = 69538.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092513 restraints weight = 44146.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092596 restraints weight = 35933.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.093174 restraints weight = 31097.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093343 restraints weight = 27799.281| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 29128 Z= 0.205 Angle : 0.588 12.490 39772 Z= 0.295 Chirality : 0.044 0.211 4629 Planarity : 0.004 0.050 5043 Dihedral : 4.381 49.834 3859 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 2.52 % Allowed : 12.31 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.29 (0.14), residues: 3531 helix: 2.34 (0.20), residues: 646 sheet: 0.16 (0.18), residues: 867 loop : -0.49 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.037 0.002 TYR C 492 PHE 0.020 0.002 PHE F 71 TRP 0.029 0.002 TRP B 104 HIS 0.029 0.001 HIS H 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (29042) covalent geometry : angle 0.58000 / 0.29 (39557) SS BOND : bond 0.00370 / 0.26 ( 43) SS BOND : angle 1.54470 / 0.91 ( 86) hydrogen bonds : bond 0.03582 / 2.30 ( 1168) hydrogen bonds : angle 5.32569 / 3.61 ( 3180) link_BETA1-4 : bond 0.00238 / 0.14 ( 15) link_BETA1-4 : angle 1.12533 / 0.77 ( 45) link_NAG-ASN : bond 0.00273 / 0.17 ( 28) link_NAG-ASN : angle 1.52560 / 0.95 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 104 TRP cc_start: 0.8007 (m-90) cc_final: 0.7584 (m-90) REVERT: A 135 PHE cc_start: 0.6418 (p90) cc_final: 0.6110 (p90) REVERT: A 224 GLU cc_start: 0.8864 (pm20) cc_final: 0.8550 (pm20) REVERT: A 266 TYR cc_start: 0.8029 (m-80) cc_final: 0.7703 (m-10) REVERT: A 272 PHE cc_start: 0.8559 (m-80) cc_final: 0.8295 (m-10) REVERT: A 323 ILE cc_start: 0.7105 (mt) cc_final: 0.6730 (tt) REVERT: A 335 PHE cc_start: 0.9166 (m-10) cc_final: 0.8843 (m-80) REVERT: A 393 TYR cc_start: 0.8928 (m-80) cc_final: 0.8585 (m-80) REVERT: A 449 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9283 (tt) REVERT: A 494 PHE cc_start: 0.8592 (m-80) cc_final: 0.7716 (m-80) REVERT: A 866 MET cc_start: 0.8498 (mtt) cc_final: 0.8201 (mtt) REVERT: A 915 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 952 ASN cc_start: 0.8309 (t0) cc_final: 0.7765 (t0) REVERT: B 202 LYS cc_start: 0.8813 (mttm) cc_final: 0.8452 (mmmm) REVERT: B 271 THR cc_start: 0.9047 (m) cc_final: 0.8129 (p) REVERT: B 295 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 348 TYR cc_start: 0.9183 (p90) cc_final: 0.8881 (p90) REVERT: B 352 ARG cc_start: 0.8698 (ttm170) cc_final: 0.8374 (ttt180) REVERT: B 433 TRP cc_start: 0.7343 (p90) cc_final: 0.6821 (p90) REVERT: B 866 MET cc_start: 0.8200 (mtm) cc_final: 0.7769 (ttm) REVERT: B 1031 LEU cc_start: 0.9153 (mt) cc_final: 0.8634 (mp) REVERT: C 206 LYS cc_start: 0.8768 (tptt) cc_final: 0.8562 (tptt) REVERT: C 266 TYR cc_start: 0.7945 (m-80) cc_final: 0.7484 (m-80) REVERT: C 350 TRP cc_start: 0.8232 (p-90) cc_final: 0.7945 (p-90) REVERT: C 367 ASN cc_start: 0.8703 (m-40) cc_final: 0.8403 (p0) REVERT: C 405 ARG cc_start: 0.8402 (ppt170) cc_final: 0.7832 (ppt170) REVERT: C 581 ILE cc_start: 0.8463 (mm) cc_final: 0.7863 (mm) REVERT: C 728 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (ptp) REVERT: C 801 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: C 855 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8841 (mt) REVERT: C 987 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 1001 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9285 (tt) REVERT: C 1026 MET cc_start: 0.8938 (tpp) cc_final: 0.8398 (ttm) REVERT: C 1047 MET cc_start: 0.8458 (ptp) cc_final: 0.8171 (ptp) REVERT: H 80 TYR cc_start: 0.9080 (m-80) cc_final: 0.8423 (m-80) REVERT: L 49 TYR cc_start: 0.7978 (p90) cc_final: 0.7607 (p90) REVERT: J 80 TYR cc_start: 0.8902 (m-80) cc_final: 0.8516 (t80) REVERT: J 106 LEU cc_start: 0.8867 (mt) cc_final: 0.8439 (tp) REVERT: K 54 ARG cc_start: 0.8332 (mtt180) cc_final: 0.8078 (ttp-170) REVERT: E 64 PHE cc_start: 0.8748 (m-80) cc_final: 0.8545 (t80) REVERT: E 95 TYR cc_start: 0.7505 (m-80) cc_final: 0.7257 (m-80) REVERT: F 4 MET cc_start: 0.6252 (mtp) cc_final: 0.5863 (mtp) outliers start: 77 outliers final: 55 residues processed: 335 average time/residue: 0.1899 time to fit residues: 102.0950 Evaluate side-chains 330 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 801 GLN Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 296 optimal weight: 0.1980 chunk 335 optimal weight: 40.0000 chunk 312 optimal weight: 30.0000 chunk 179 optimal weight: 3.9990 chunk 325 optimal weight: 50.0000 chunk 2 optimal weight: 7.9990 chunk 348 optimal weight: 0.6980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.4231 r_free = 0.4231 target = 0.145626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090229 restraints weight = 69794.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090332 restraints weight = 46505.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089498 restraints weight = 31169.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090096 restraints weight = 32768.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090537 restraints weight = 26898.733| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29128 Z= 0.175 Angle : 0.568 11.429 39772 Z= 0.286 Chirality : 0.044 0.203 4629 Planarity : 0.004 0.053 5043 Dihedral : 4.254 49.737 3855 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 2.45 % Allowed : 13.03 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.31 (0.14), residues: 3531 helix: 2.48 (0.20), residues: 640 sheet: 0.13 (0.18), residues: 870 loop : -0.50 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.022 0.001 TYR C 492 PHE 0.017 0.001 PHE C 389 TRP 0.029 0.001 TRP B 104 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (29042) covalent geometry : angle 0.56047 / 0.28 (39557) SS BOND : bond 0.00392 / 0.30 ( 43) SS BOND : angle 1.33186 / 0.81 ( 86) hydrogen bonds : bond 0.03524 / 2.25 ( 1168) hydrogen bonds : angle 5.30403 / 3.60 ( 3180) link_BETA1-4 : bond 0.00261 / 0.15 ( 15) link_BETA1-4 : angle 1.09431 / 0.75 ( 45) link_NAG-ASN : bond 0.00243 / 0.15 ( 28) link_NAG-ASN : angle 1.46451 / 0.92 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 282 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7986 (m-90) cc_final: 0.7655 (m-90) REVERT: A 135 PHE cc_start: 0.6372 (p90) cc_final: 0.6069 (p90) REVERT: A 224 GLU cc_start: 0.8904 (pm20) cc_final: 0.8587 (pm20) REVERT: A 266 TYR cc_start: 0.8165 (m-80) cc_final: 0.7914 (m-10) REVERT: A 272 PHE cc_start: 0.8532 (m-80) cc_final: 0.8303 (m-80) REVERT: A 335 PHE cc_start: 0.9121 (m-10) cc_final: 0.8732 (m-10) REVERT: A 393 TYR cc_start: 0.8844 (m-80) cc_final: 0.8542 (m-80) REVERT: A 448 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.4880 (t80) REVERT: A 449 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9283 (tt) REVERT: A 494 PHE cc_start: 0.8610 (m-80) cc_final: 0.7726 (m-80) REVERT: A 866 MET cc_start: 0.8499 (mtt) cc_final: 0.8199 (mtt) REVERT: A 915 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 952 ASN cc_start: 0.8362 (t0) cc_final: 0.7792 (t0) REVERT: B 53 ASP cc_start: 0.7757 (t70) cc_final: 0.7337 (t70) REVERT: B 202 LYS cc_start: 0.8799 (mttm) cc_final: 0.8451 (mmmm) REVERT: B 271 THR cc_start: 0.8807 (m) cc_final: 0.8181 (p) REVERT: B 295 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: B 348 TYR cc_start: 0.9194 (p90) cc_final: 0.8838 (p90) REVERT: B 433 TRP cc_start: 0.7292 (p90) cc_final: 0.6665 (p90) REVERT: B 853 ASN cc_start: 0.8391 (t0) cc_final: 0.7712 (t0) REVERT: B 866 MET cc_start: 0.8345 (mtm) cc_final: 0.7921 (ttm) REVERT: B 1031 LEU cc_start: 0.9212 (mt) cc_final: 0.8696 (mp) REVERT: C 266 TYR cc_start: 0.7774 (m-80) cc_final: 0.7437 (m-80) REVERT: C 367 ASN cc_start: 0.8702 (m-40) cc_final: 0.8415 (p0) REVERT: C 389 PHE cc_start: 0.8124 (m-80) cc_final: 0.7859 (m-80) REVERT: C 405 ARG cc_start: 0.8413 (ppt170) cc_final: 0.7832 (ppt170) REVERT: C 433 TRP cc_start: 0.8361 (p90) cc_final: 0.8160 (p90) REVERT: C 581 ILE cc_start: 0.8440 (mm) cc_final: 0.7814 (mm) REVERT: C 728 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8891 (ptp) REVERT: C 855 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 987 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 1001 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9276 (tt) REVERT: C 1026 MET cc_start: 0.8948 (tpp) cc_final: 0.8386 (ttm) REVERT: H 80 TYR cc_start: 0.8951 (m-80) cc_final: 0.8312 (m-80) REVERT: L 44 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7458 (Cg_exo) REVERT: L 45 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8217 (mmm160) REVERT: J 80 TYR cc_start: 0.8800 (m-80) cc_final: 0.8453 (t80) REVERT: J 106 LEU cc_start: 0.8839 (mt) cc_final: 0.8407 (tp) REVERT: K 24 ARG cc_start: 0.9180 (mtm-85) cc_final: 0.8772 (mpp-170) REVERT: E 48 MET cc_start: 0.4789 (ppp) cc_final: 0.3759 (pmm) REVERT: E 95 TYR cc_start: 0.7480 (m-80) cc_final: 0.7166 (m-80) REVERT: F 4 MET cc_start: 0.6314 (mtp) cc_final: 0.5904 (mtp) REVERT: F 38 GLN cc_start: 0.9590 (tt0) cc_final: 0.9282 (tp40) outliers start: 75 outliers final: 55 residues processed: 330 average time/residue: 0.1891 time to fit residues: 100.0192 Evaluate side-chains 329 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 99 optimal weight: 0.0980 chunk 273 optimal weight: 0.9980 chunk 327 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 350 optimal weight: 50.0000 chunk 230 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090946 restraints weight = 70065.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091205 restraints weight = 42630.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090855 restraints weight = 29930.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091215 restraints weight = 29079.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091451 restraints weight = 25482.573| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29128 Z= 0.110 Angle : 0.548 13.020 39772 Z= 0.273 Chirality : 0.043 0.211 4629 Planarity : 0.004 0.052 5043 Dihedral : 4.102 49.630 3855 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 13.75 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.44 (0.14), residues: 3531 helix: 2.72 (0.21), residues: 639 sheet: 0.18 (0.18), residues: 861 loop : -0.44 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 61 TYR 0.022 0.001 TYR C 492 PHE 0.023 0.001 PHE B 92 TRP 0.025 0.001 TRP K 35 HIS 0.003 0.001 HIS E 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (29042) covalent geometry : angle 0.54213 / 0.27 (39557) SS BOND : bond 0.00286 / 0.21 ( 43) SS BOND : angle 1.08601 / 0.67 ( 86) hydrogen bonds : bond 0.03206 / 2.06 ( 1168) hydrogen bonds : angle 5.10781 / 3.46 ( 3180) link_BETA1-4 : bond 0.00339 / 0.19 ( 15) link_BETA1-4 : angle 1.04865 / 0.72 ( 45) link_NAG-ASN : bond 0.00199 / 0.11 ( 28) link_NAG-ASN : angle 1.34275 / 0.85 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7929 (m-90) cc_final: 0.7652 (m-90) REVERT: A 135 PHE cc_start: 0.6391 (p90) cc_final: 0.6092 (p90) REVERT: A 224 GLU cc_start: 0.8897 (pm20) cc_final: 0.8587 (pm20) REVERT: A 266 TYR cc_start: 0.8165 (m-80) cc_final: 0.7944 (m-10) REVERT: A 272 PHE cc_start: 0.8509 (m-80) cc_final: 0.8302 (m-10) REVERT: A 297 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8626 (ttmm) REVERT: A 335 PHE cc_start: 0.9142 (m-10) cc_final: 0.8757 (m-10) REVERT: A 393 TYR cc_start: 0.8921 (m-80) cc_final: 0.8637 (m-80) REVERT: A 448 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.5079 (t80) REVERT: A 449 LEU cc_start: 0.9714 (mt) cc_final: 0.9284 (tt) REVERT: A 494 PHE cc_start: 0.8611 (m-80) cc_final: 0.7797 (m-80) REVERT: A 866 MET cc_start: 0.8498 (mtt) cc_final: 0.8199 (mtt) REVERT: A 915 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 952 ASN cc_start: 0.8359 (t0) cc_final: 0.7767 (t0) REVERT: A 993 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8883 (mt) REVERT: B 202 LYS cc_start: 0.8811 (mttm) cc_final: 0.8466 (mmmm) REVERT: B 271 THR cc_start: 0.8812 (m) cc_final: 0.8200 (p) REVERT: B 295 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: B 348 TYR cc_start: 0.9266 (p90) cc_final: 0.8933 (p90) REVERT: B 393 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: B 853 ASN cc_start: 0.8483 (t0) cc_final: 0.8084 (t0) REVERT: B 866 MET cc_start: 0.8312 (mtm) cc_final: 0.7903 (ttm) REVERT: B 1026 MET cc_start: 0.8782 (tpp) cc_final: 0.8122 (ttm) REVERT: C 54 LEU cc_start: 0.8821 (mm) cc_final: 0.8338 (pt) REVERT: C 206 LYS cc_start: 0.8834 (tptt) cc_final: 0.8572 (tptp) REVERT: C 266 TYR cc_start: 0.7812 (m-80) cc_final: 0.7475 (m-80) REVERT: C 267 LEU cc_start: 0.8586 (pt) cc_final: 0.8269 (pt) REVERT: C 367 ASN cc_start: 0.8804 (m-40) cc_final: 0.8534 (p0) REVERT: C 389 PHE cc_start: 0.8079 (m-80) cc_final: 0.7847 (m-80) REVERT: C 405 ARG cc_start: 0.8404 (ppt170) cc_final: 0.7850 (ppt170) REVERT: C 433 TRP cc_start: 0.8294 (p90) cc_final: 0.8060 (p90) REVERT: C 581 ILE cc_start: 0.8446 (mm) cc_final: 0.7819 (mm) REVERT: C 855 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8841 (mt) REVERT: C 1001 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9288 (tt) REVERT: C 1026 MET cc_start: 0.8944 (tpp) cc_final: 0.8447 (ttm) REVERT: J 80 TYR cc_start: 0.8907 (m-80) cc_final: 0.8637 (t80) REVERT: J 106 LEU cc_start: 0.8888 (mt) cc_final: 0.8459 (tp) REVERT: K 54 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8112 (ttp-110) REVERT: E 48 MET cc_start: 0.4819 (ppp) cc_final: 0.3663 (pmm) REVERT: E 95 TYR cc_start: 0.7524 (m-80) cc_final: 0.7248 (m-80) REVERT: F 4 MET cc_start: 0.6244 (mtp) cc_final: 0.5841 (mtp) outliers start: 60 outliers final: 41 residues processed: 323 average time/residue: 0.1797 time to fit residues: 93.5944 Evaluate side-chains 314 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 35 optimal weight: 4.9990 chunk 351 optimal weight: 50.0000 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 288 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 294 optimal weight: 20.0000 chunk 225 optimal weight: 40.0000 chunk 252 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.4252 r_free = 0.4252 target = 0.151597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097022 restraints weight = 69784.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095390 restraints weight = 45223.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096100 restraints weight = 35731.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096765 restraints weight = 30210.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096972 restraints weight = 25773.285| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29128 Z= 0.126 Angle : 0.562 13.130 39772 Z= 0.281 Chirality : 0.043 0.208 4629 Planarity : 0.004 0.059 5043 Dihedral : 4.072 49.433 3855 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 1.77 % Allowed : 14.11 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.46 (0.14), residues: 3531 helix: 2.78 (0.21), residues: 632 sheet: 0.17 (0.18), residues: 862 loop : -0.41 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 38 TYR 0.019 0.001 TYR A1064 PHE 0.019 0.001 PHE B 86 TRP 0.030 0.001 TRP K 35 HIS 0.003 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (29042) covalent geometry : angle 0.55395 / 0.28 (39557) SS BOND : bond 0.00322 / 0.25 ( 43) SS BOND : angle 1.68221 / 0.81 ( 86) hydrogen bonds : bond 0.03203 / 2.05 ( 1168) hydrogen bonds : angle 5.14048 / 3.49 ( 3180) link_BETA1-4 : bond 0.00289 / 0.16 ( 15) link_BETA1-4 : angle 1.06099 / 0.72 ( 45) link_NAG-ASN : bond 0.00185 / 0.11 ( 28) link_NAG-ASN : angle 1.33223 / 0.85 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7893 (m-90) cc_final: 0.7669 (m-90) REVERT: A 135 PHE cc_start: 0.6278 (p90) cc_final: 0.5962 (p90) REVERT: A 224 GLU cc_start: 0.8841 (pm20) cc_final: 0.8550 (pm20) REVERT: A 335 PHE cc_start: 0.8969 (m-10) cc_final: 0.8572 (m-10) REVERT: A 393 TYR cc_start: 0.8695 (m-80) cc_final: 0.8428 (m-80) REVERT: A 448 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.3643 (t80) REVERT: A 449 LEU cc_start: 0.9633 (mt) cc_final: 0.9221 (tt) REVERT: A 494 PHE cc_start: 0.8339 (m-80) cc_final: 0.7629 (m-80) REVERT: A 866 MET cc_start: 0.8448 (mtt) cc_final: 0.8166 (mtt) REVERT: A 915 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 952 ASN cc_start: 0.8340 (t0) cc_final: 0.7761 (t0) REVERT: B 202 LYS cc_start: 0.8782 (mttm) cc_final: 0.8427 (mmmm) REVERT: B 271 THR cc_start: 0.8841 (m) cc_final: 0.8223 (p) REVERT: B 295 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 348 TYR cc_start: 0.9137 (p90) cc_final: 0.8883 (p90) REVERT: B 853 ASN cc_start: 0.8408 (t0) cc_final: 0.8064 (t0) REVERT: B 866 MET cc_start: 0.8247 (mtm) cc_final: 0.7864 (ttm) REVERT: B 1026 MET cc_start: 0.8672 (tpp) cc_final: 0.8006 (ttm) REVERT: C 54 LEU cc_start: 0.8806 (mm) cc_final: 0.8317 (pt) REVERT: C 206 LYS cc_start: 0.8684 (tptt) cc_final: 0.8397 (tptp) REVERT: C 266 TYR cc_start: 0.7705 (m-80) cc_final: 0.7434 (m-80) REVERT: C 267 LEU cc_start: 0.8495 (pt) cc_final: 0.8192 (pt) REVERT: C 367 ASN cc_start: 0.8659 (m-40) cc_final: 0.8454 (p0) REVERT: C 405 ARG cc_start: 0.8463 (ppt170) cc_final: 0.7918 (ppt170) REVERT: C 433 TRP cc_start: 0.8195 (p90) cc_final: 0.7974 (p90) REVERT: C 581 ILE cc_start: 0.8418 (mm) cc_final: 0.7838 (mm) REVERT: C 855 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (mt) REVERT: C 1001 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9272 (tt) REVERT: C 1026 MET cc_start: 0.8911 (tpp) cc_final: 0.8367 (ttm) REVERT: H 80 TYR cc_start: 0.8819 (m-80) cc_final: 0.8173 (m-80) REVERT: J 80 TYR cc_start: 0.8746 (m-80) cc_final: 0.8512 (t80) REVERT: J 106 LEU cc_start: 0.8830 (mt) cc_final: 0.8413 (tp) REVERT: E 40 MET cc_start: 0.6167 (mmm) cc_final: 0.5342 (mmm) REVERT: E 48 MET cc_start: 0.4684 (ppp) cc_final: 0.3591 (pmm) REVERT: E 95 TYR cc_start: 0.7417 (m-80) cc_final: 0.7180 (m-80) REVERT: F 4 MET cc_start: 0.5929 (mtp) cc_final: 0.5522 (mtp) REVERT: F 46 LEU cc_start: 0.7344 (tp) cc_final: 0.6284 (mp) outliers start: 54 outliers final: 47 residues processed: 311 average time/residue: 0.1587 time to fit residues: 79.8751 Evaluate side-chains 316 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 1 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 60 optimal weight: 0.0010 chunk 241 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 43 optimal weight: 0.0070 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 overall best weight: 2.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 59 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.4230 r_free = 0.4230 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093058 restraints weight = 69709.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093710 restraints weight = 43943.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093315 restraints weight = 27749.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093832 restraints weight = 27383.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094015 restraints weight = 24441.593| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29128 Z= 0.210 Angle : 0.603 13.149 39772 Z= 0.302 Chirality : 0.044 0.210 4629 Planarity : 0.004 0.086 5043 Dihedral : 4.231 49.401 3855 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 1.87 % Allowed : 14.27 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.34 (0.14), residues: 3531 helix: 2.54 (0.21), residues: 638 sheet: 0.09 (0.18), residues: 860 loop : -0.44 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 24 TYR 0.020 0.001 TYR C1064 PHE 0.025 0.002 PHE A 272 TRP 0.024 0.001 TRP K 35 HIS 0.004 0.001 HIS C1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (29042) covalent geometry : angle 0.59417 / 0.30 (39557) SS BOND : bond 0.00408 / 0.31 ( 43) SS BOND : angle 1.83076 / 0.93 ( 86) hydrogen bonds : bond 0.03558 / 2.27 ( 1168) hydrogen bonds : angle 5.29099 / 3.59 ( 3180) link_BETA1-4 : bond 0.00203 / 0.11 ( 15) link_BETA1-4 : angle 1.12021 / 0.76 ( 45) link_NAG-ASN : bond 0.00260 / 0.17 ( 28) link_NAG-ASN : angle 1.43460 / 0.90 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 104 TRP cc_start: 0.8006 (m-90) cc_final: 0.7709 (m-90) REVERT: A 135 PHE cc_start: 0.6580 (p90) cc_final: 0.6219 (p90) REVERT: A 224 GLU cc_start: 0.8909 (pm20) cc_final: 0.8601 (pm20) REVERT: A 335 PHE cc_start: 0.9049 (m-10) cc_final: 0.8652 (m-10) REVERT: A 393 TYR cc_start: 0.8882 (m-80) cc_final: 0.8622 (m-80) REVERT: A 448 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.3952 (t80) REVERT: A 449 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9262 (tt) REVERT: A 494 PHE cc_start: 0.8531 (m-80) cc_final: 0.7773 (m-80) REVERT: A 866 MET cc_start: 0.8463 (mtt) cc_final: 0.8197 (mtt) REVERT: A 915 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 202 LYS cc_start: 0.8806 (mttm) cc_final: 0.8269 (mtpp) REVERT: B 271 THR cc_start: 0.8894 (m) cc_final: 0.8300 (p) REVERT: B 295 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: B 348 TYR cc_start: 0.9270 (p90) cc_final: 0.8925 (p90) REVERT: B 853 ASN cc_start: 0.8521 (t0) cc_final: 0.8214 (t0) REVERT: B 866 MET cc_start: 0.8264 (mtm) cc_final: 0.7863 (ttm) REVERT: C 54 LEU cc_start: 0.8797 (mm) cc_final: 0.8352 (pt) REVERT: C 206 LYS cc_start: 0.8794 (tptt) cc_final: 0.8485 (tptp) REVERT: C 266 TYR cc_start: 0.7833 (m-80) cc_final: 0.7507 (m-80) REVERT: C 267 LEU cc_start: 0.8622 (pt) cc_final: 0.8313 (pt) REVERT: C 324 VAL cc_start: 0.8307 (t) cc_final: 0.7807 (p) REVERT: C 367 ASN cc_start: 0.8769 (m-40) cc_final: 0.8530 (p0) REVERT: C 405 ARG cc_start: 0.8433 (ppt170) cc_final: 0.7868 (ppt170) REVERT: C 433 TRP cc_start: 0.8374 (p90) cc_final: 0.8129 (p90) REVERT: C 581 ILE cc_start: 0.8471 (mm) cc_final: 0.7863 (mm) REVERT: C 855 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 987 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 1001 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9315 (tt) REVERT: C 1026 MET cc_start: 0.8953 (tpp) cc_final: 0.8357 (ttm) REVERT: C 1047 MET cc_start: 0.8397 (ptp) cc_final: 0.8155 (ptp) REVERT: H 53 PRO cc_start: 0.9334 (Cg_exo) cc_final: 0.8792 (Cg_endo) REVERT: H 80 TYR cc_start: 0.8902 (m-80) cc_final: 0.8280 (m-80) REVERT: J 80 TYR cc_start: 0.8867 (m-80) cc_final: 0.8600 (t80) REVERT: E 48 MET cc_start: 0.4874 (ppp) cc_final: 0.3971 (pmm) REVERT: E 95 TYR cc_start: 0.7537 (m-80) cc_final: 0.7231 (m-80) REVERT: F 4 MET cc_start: 0.6170 (mtp) cc_final: 0.5744 (mtp) REVERT: F 46 LEU cc_start: 0.7555 (tp) cc_final: 0.6552 (mp) outliers start: 57 outliers final: 51 residues processed: 316 average time/residue: 0.1714 time to fit residues: 87.0997 Evaluate side-chains 321 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 220 optimal weight: 0.4980 chunk 307 optimal weight: 50.0000 chunk 156 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 243 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.4245 r_free = 0.4245 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095205 restraints weight = 70042.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095789 restraints weight = 44990.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095286 restraints weight = 29202.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095791 restraints weight = 28982.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096013 restraints weight = 25189.326| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29128 Z= 0.128 Angle : 0.581 13.564 39772 Z= 0.289 Chirality : 0.043 0.224 4629 Planarity : 0.004 0.062 5043 Dihedral : 4.158 49.340 3855 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 1.77 % Allowed : 14.50 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.41 (0.14), residues: 3531 helix: 2.68 (0.21), residues: 638 sheet: 0.12 (0.18), residues: 862 loop : -0.43 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 61 TYR 0.021 0.001 TYR A 37 PHE 0.023 0.001 PHE B 92 TRP 0.036 0.001 TRP C 350 HIS 0.004 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (29042) covalent geometry : angle 0.57324 / 0.29 (39557) SS BOND : bond 0.00323 / 0.26 ( 43) SS BOND : angle 1.55100 / 0.79 ( 86) hydrogen bonds : bond 0.03291 / 2.09 ( 1168) hydrogen bonds : angle 5.20328 / 3.53 ( 3180) link_BETA1-4 : bond 0.00287 / 0.16 ( 15) link_BETA1-4 : angle 1.04938 / 0.72 ( 45) link_NAG-ASN : bond 0.00195 / 0.12 ( 28) link_NAG-ASN : angle 1.33601 / 0.85 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.95 seconds wall clock time: 93 minutes 23.99 seconds (5603.99 seconds total)