Starting phenix.real_space_refine on Mon Aug 25 14:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_13873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_13873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_13873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_13873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9m_13873/08_2025/7q9m_13873.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.73, per 1000 atoms: 0.20 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: 2.33 Conformation dependent library (CDL) restraints added in 990.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.05 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: 5.64 Time building geometry restraints manager: 3.15 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 - 21.64: 17160 21.64 - 43.28: 452 43.28 - 64.92: 90 64.92 - 86.57: 25 86.57 - 108.21: 9 Dihedral angle restraints: 17736 sinusoidal: 7276 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 17733 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: 7.680 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.660 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 10.543 108.208 10885 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 aren 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 covalent geometry : bond 0.00409 (29042) covalent geometry : angle 0.56457 (39557) SS BOND : bond 0.00253 ( 43) SS BOND : angle 0.63801 ( 86) hydrogen bonds : bond 0.13459 ( 1168) hydrogen bonds : angle 7.02438 ( 3180) link_BETA1-4 : bond 0.00268 ( 15) link_BETA1-4 : angle 1.39448 ( 45) link_NAG-ASN : bond 0.00328 ( 28) link_NAG-ASN : angle 1.76501 ( 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 : 1.493 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: 0.1840 time to fit residues: 164.8958 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 : 1.026 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 853 ASN C 447 ASN C 652 HIS C 911 ASN ** H 59 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.146018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087965 restraints weight = 70077.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089428 restraints weight = 41015.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089814 restraints weight = 26127.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090167 restraints weight = 22971.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090394 restraints weight = 20948.704| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29128 Z= 0.140 Angle : 0.591 9.689 39772 Z= 0.300 Chirality : 0.044 0.238 4629 Planarity : 0.004 0.053 5043 Dihedral : 7.013 72.313 4761 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 1.67 % Allowed : 9.20 % Favored : 89.13 % 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 aren not related in a simple way. whole: 0.46 (0.14), residues: 3531 helix: 2.35 (0.20), residues: 670 sheet: 0.21 (0.17), residues: 859 loop : -0.32 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 98 TYR 0.031 0.002 TYR H 60 PHE 0.020 0.002 PHE B 194 TRP 0.033 0.003 TRP B 104 HIS 0.011 0.001 HIS J 99 Details of bonding type rmsd covalent geometry : bond 0.00322 (29042) covalent geometry : angle 0.58075 (39557) SS BOND : bond 0.00340 ( 43) SS BOND : angle 1.54638 ( 86) hydrogen bonds : bond 0.04093 ( 1168) hydrogen bonds : angle 5.72821 ( 3180) link_BETA1-4 : bond 0.00447 ( 15) link_BETA1-4 : angle 1.34736 ( 45) link_NAG-ASN : bond 0.00233 ( 28) link_NAG-ASN : angle 1.74737 ( 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 416 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.912 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: 0.7931 (m-90) cc_final: 0.7545 (m-90) REVERT: A 224 GLU cc_start: 0.8713 (pm20) cc_final: 0.8420 (pm20) REVERT: A 266 TYR cc_start: 0.7963 (m-80) cc_final: 0.7700 (m-80) REVERT: A 272 PHE cc_start: 0.8691 (m-80) cc_final: 0.8213 (m-10) REVERT: A 335 PHE cc_start: 0.9140 (m-10) cc_final: 0.8929 (m-10) REVERT: A 393 TYR cc_start: 0.9050 (m-80) cc_final: 0.8564 (m-10) REVERT: A 494 PHE cc_start: 0.7912 (m-80) cc_final: 0.7542 (m-80) REVERT: A 652 HIS cc_start: 0.7956 (t70) cc_final: 0.7731 (t70) REVERT: A 728 MET cc_start: 0.8428 (ptm) cc_final: 0.8160 (ptm) REVERT: A 866 MET cc_start: 0.8439 (mtt) cc_final: 0.8102 (mtt) REVERT: B 104 TRP cc_start: 0.6476 (m-90) cc_final: 0.6203 (m-90) REVERT: B 129 LYS cc_start: 0.8266 (mttt) cc_final: 0.7863 (mmmt) REVERT: B 202 LYS cc_start: 0.8772 (mttm) cc_final: 0.8388 (mmmm) REVERT: B 295 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: B 335 PHE cc_start: 0.8027 (m-80) cc_final: 0.7723 (m-80) REVERT: B 433 TRP cc_start: 0.7252 (p90) cc_final: 0.6881 (p90) REVERT: B 803 LEU cc_start: 0.8976 (mt) cc_final: 0.8695 (mm) REVERT: B 813 SER cc_start: 0.9045 (p) cc_final: 0.8814 (m) REVERT: B 855 LEU cc_start: 0.8392 (mp) cc_final: 0.8066 (mp) REVERT: B 985 GLU cc_start: 0.8514 (mp0) cc_final: 0.8301 (mp0) REVERT: B 987 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: B 1080 HIS cc_start: 0.7758 (t70) cc_final: 0.7483 (t70) REVERT: C 262 TYR cc_start: 0.6685 (p90) cc_final: 0.6228 (p90) REVERT: C 266 TYR cc_start: 0.7384 (m-80) cc_final: 0.7038 (m-80) REVERT: C 367 ASN cc_start: 0.8697 (m-40) cc_final: 0.8239 (p0) REVERT: C 397 PHE cc_start: 0.8043 (p90) cc_final: 0.7742 (p90) REVERT: C 399 ILE cc_start: 0.7825 (pt) cc_final: 0.7443 (pt) REVERT: C 433 TRP cc_start: 0.8338 (p90) cc_final: 0.7918 (p90) REVERT: C 461 PHE cc_start: 0.8959 (m-80) cc_final: 0.8725 (m-80) REVERT: C 581 ILE cc_start: 0.8394 (mm) cc_final: 0.7764 (mm) REVERT: C 801 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6980 (mt0) REVERT: C 892 GLN cc_start: 0.8499 (pm20) cc_final: 0.8265 (pm20) REVERT: C 1001 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9347 (tt) REVERT: L 49 TYR cc_start: 0.8221 (p90) cc_final: 0.7822 (p90) REVERT: J 109 ASP cc_start: 0.7866 (p0) cc_final: 0.7218 (p0) REVERT: K 4 MET cc_start: 0.9171 (mmm) cc_final: 0.8884 (mmm) REVERT: K 54 ARG cc_start: 0.8335 (mtt180) cc_final: 0.7811 (tmm-80) REVERT: E 95 TYR cc_start: 0.7607 (m-80) cc_final: 0.7348 (m-80) REVERT: F 4 MET cc_start: 0.6375 (mtp) cc_final: 0.5983 (mtp) REVERT: F 46 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7191 (mp) outliers start: 51 outliers final: 26 residues processed: 392 average time/residue: 0.1818 time to fit residues: 110.7574 Evaluate side-chains 321 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 L residue 37 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 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: 0.5980 chunk 50 optimal weight: 0.0030 chunk 341 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 350 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 385 ASN B 898 GLN B 932 GLN C 898 GLN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN K 27 GLN E 27 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.145112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088269 restraints weight = 70170.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088627 restraints weight = 44238.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088242 restraints weight = 30392.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088635 restraints weight = 30626.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088818 restraints weight = 27390.459| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29128 Z= 0.151 Angle : 0.583 10.056 39772 Z= 0.294 Chirality : 0.044 0.228 4629 Planarity : 0.004 0.061 5043 Dihedral : 6.073 53.864 4759 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 2.13 % Allowed : 10.18 % Favored : 87.69 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3531 helix: 2.31 (0.20), residues: 672 sheet: 0.18 (0.17), residues: 883 loop : -0.41 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 98 TYR 0.021 0.002 TYR H 60 PHE 0.018 0.001 PHE F 71 TRP 0.023 0.002 TRP E 36 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00350 (29042) covalent geometry : angle 0.57221 (39557) SS BOND : bond 0.00668 ( 43) SS BOND : angle 1.68819 ( 86) hydrogen bonds : bond 0.03671 ( 1168) hydrogen bonds : angle 5.49889 ( 3180) link_BETA1-4 : bond 0.00288 ( 15) link_BETA1-4 : angle 1.42007 ( 45) link_NAG-ASN : bond 0.00234 ( 28) link_NAG-ASN : angle 1.70736 ( 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: 65 poor density : 314 time to evaluate : 0.873 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: A 104 TRP cc_start: 0.7832 (m-90) cc_final: 0.7362 (m-90) REVERT: A 224 GLU cc_start: 0.8754 (pm20) cc_final: 0.8421 (pm20) REVERT: A 266 TYR cc_start: 0.7878 (m-80) cc_final: 0.7648 (m-10) REVERT: A 272 PHE cc_start: 0.8627 (m-80) cc_final: 0.8316 (m-10) REVERT: A 335 PHE cc_start: 0.9075 (m-10) cc_final: 0.8843 (m-10) REVERT: A 393 TYR cc_start: 0.8896 (m-80) cc_final: 0.8431 (m-10) REVERT: A 449 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9242 (tt) REVERT: A 494 PHE cc_start: 0.7891 (m-80) cc_final: 0.7498 (m-80) REVERT: A 866 MET cc_start: 0.8490 (mtt) cc_final: 0.8166 (mtt) REVERT: A 915 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 952 ASN cc_start: 0.7933 (t0) cc_final: 0.7524 (t0) REVERT: B 202 LYS cc_start: 0.8768 (mttm) cc_final: 0.8392 (mmmm) REVERT: B 295 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: B 335 PHE cc_start: 0.8034 (m-80) cc_final: 0.7718 (m-80) REVERT: B 433 TRP cc_start: 0.7189 (p90) cc_final: 0.6752 (p90) REVERT: B 855 LEU cc_start: 0.8442 (mp) cc_final: 0.8065 (mp) REVERT: B 866 MET cc_start: 0.8182 (mtm) cc_final: 0.7724 (ttm) REVERT: B 985 GLU cc_start: 0.8677 (mp0) cc_final: 0.8475 (mp0) REVERT: B 987 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: B 1026 MET cc_start: 0.8741 (tpp) cc_final: 0.8280 (ttm) REVERT: C 206 LYS cc_start: 0.8649 (tptt) cc_final: 0.8383 (tptt) REVERT: C 367 ASN cc_start: 0.8719 (m-40) cc_final: 0.8362 (p0) REVERT: C 399 ILE cc_start: 0.7855 (pt) cc_final: 0.7534 (pt) REVERT: C 405 ARG cc_start: 0.8302 (ppt170) cc_final: 0.7943 (ppt170) REVERT: C 433 TRP cc_start: 0.8346 (p90) cc_final: 0.7847 (p90) REVERT: C 581 ILE cc_start: 0.8398 (mm) cc_final: 0.7779 (mm) REVERT: C 855 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8885 (mt) REVERT: C 892 GLN cc_start: 0.8551 (pm20) cc_final: 0.8295 (pm20) REVERT: C 1001 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9309 (tt) REVERT: C 1047 MET cc_start: 0.8413 (ptp) cc_final: 0.8202 (ptp) REVERT: L 49 TYR cc_start: 0.8135 (p90) cc_final: 0.7778 (p90) REVERT: L 89 GLN cc_start: 0.3197 (OUTLIER) cc_final: 0.2508 (tp40) REVERT: J 48 MET cc_start: 0.8390 (mpp) cc_final: 0.8100 (mpp) REVERT: J 80 TYR cc_start: 0.8783 (m-80) cc_final: 0.8430 (t80) REVERT: J 106 LEU cc_start: 0.8768 (mt) cc_final: 0.8461 (mt) REVERT: K 54 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7915 (ttp-170) REVERT: E 95 TYR cc_start: 0.7467 (m-80) cc_final: 0.7040 (m-80) REVERT: F 4 MET cc_start: 0.6087 (mtp) cc_final: 0.5506 (mtp) REVERT: F 46 LEU cc_start: 0.7771 (tp) cc_final: 0.7083 (mp) outliers start: 65 outliers final: 39 residues processed: 355 average time/residue: 0.1777 time to fit residues: 100.2433 Evaluate side-chains 323 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 960 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 192 PHE 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 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 855 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 38 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU 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: 20.0000 chunk 173 optimal weight: 0.7980 chunk 310 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 203 optimal weight: 0.0370 chunk 24 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 330 optimal weight: 40.0000 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 ASN B 853 ASN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN F 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.145611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085393 restraints weight = 69853.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088309 restraints weight = 34604.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089100 restraints weight = 24306.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089656 restraints weight = 18635.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089921 restraints weight = 16212.123| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29128 Z= 0.119 Angle : 0.559 11.732 39772 Z= 0.281 Chirality : 0.044 0.231 4629 Planarity : 0.004 0.057 5043 Dihedral : 5.349 50.464 4757 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.90 % Allowed : 11.10 % Favored : 87.00 % 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 aren not related in a simple way. whole: 0.42 (0.14), residues: 3531 helix: 2.36 (0.20), residues: 672 sheet: 0.20 (0.17), residues: 871 loop : -0.38 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.020 0.001 TYR H 60 PHE 0.033 0.001 PHE F 71 TRP 0.032 0.001 TRP B 104 HIS 0.004 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00269 (29042) covalent geometry : angle 0.55253 (39557) SS BOND : bond 0.00337 ( 43) SS BOND : angle 0.92379 ( 86) hydrogen bonds : bond 0.03386 ( 1168) hydrogen bonds : angle 5.29610 ( 3180) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.38543 ( 45) link_NAG-ASN : bond 0.00211 ( 28) link_NAG-ASN : angle 1.59536 ( 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 363 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 1.129 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: 0.7861 (m-90) cc_final: 0.7316 (m-90) REVERT: A 135 PHE cc_start: 0.6409 (p90) cc_final: 0.6114 (p90) REVERT: A 224 GLU cc_start: 0.8738 (pm20) cc_final: 0.8410 (pm20) REVERT: A 266 TYR cc_start: 0.7777 (m-80) cc_final: 0.7504 (m-10) REVERT: A 335 PHE cc_start: 0.9179 (m-10) cc_final: 0.8907 (m-10) REVERT: A 393 TYR cc_start: 0.9032 (m-80) cc_final: 0.8547 (m-10) REVERT: A 449 LEU cc_start: 0.9774 (mt) cc_final: 0.9316 (tt) REVERT: A 494 PHE cc_start: 0.7945 (m-80) cc_final: 0.7608 (m-80) REVERT: A 529 ASN cc_start: 0.8499 (t0) cc_final: 0.8285 (t0) REVERT: A 866 MET cc_start: 0.8431 (mtt) cc_final: 0.8108 (mtt) REVERT: A 952 ASN cc_start: 0.7902 (t0) cc_final: 0.7534 (t0) REVERT: B 202 LYS cc_start: 0.8763 (mttm) cc_final: 0.8407 (mmmm) REVERT: B 295 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: B 335 PHE cc_start: 0.8005 (m-80) cc_final: 0.7677 (m-80) REVERT: B 348 TYR cc_start: 0.9190 (p90) cc_final: 0.8882 (p90) REVERT: B 433 TRP cc_start: 0.7244 (p90) cc_final: 0.6781 (p90) REVERT: B 855 LEU cc_start: 0.8342 (mp) cc_final: 0.7991 (mp) REVERT: B 866 MET cc_start: 0.8105 (mtm) cc_final: 0.7768 (ttm) REVERT: B 987 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: B 1026 MET cc_start: 0.8789 (tpp) cc_final: 0.7967 (ttm) REVERT: B 1031 LEU cc_start: 0.9198 (mt) cc_final: 0.8675 (mp) REVERT: C 266 TYR cc_start: 0.7454 (m-80) cc_final: 0.7082 (m-80) REVERT: C 389 PHE cc_start: 0.8014 (m-80) cc_final: 0.7748 (m-80) REVERT: C 399 ILE cc_start: 0.7787 (pt) cc_final: 0.7466 (pt) REVERT: C 405 ARG cc_start: 0.8367 (ppt170) cc_final: 0.7897 (ppt170) REVERT: C 581 ILE cc_start: 0.8364 (mm) cc_final: 0.7785 (mm) REVERT: C 728 MET cc_start: 0.9183 (ptp) cc_final: 0.8967 (ptp) REVERT: C 855 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8833 (mt) REVERT: C 892 GLN cc_start: 0.8486 (pm20) cc_final: 0.8274 (pm20) REVERT: C 1001 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9315 (tt) REVERT: C 1026 MET cc_start: 0.8885 (tpp) cc_final: 0.8296 (ttm) REVERT: H 38 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8001 (ttt-90) REVERT: H 64 PHE cc_start: 0.8020 (m-80) cc_final: 0.7687 (m-80) REVERT: L 49 TYR cc_start: 0.8157 (p90) cc_final: 0.7777 (p90) REVERT: J 48 MET cc_start: 0.8537 (mpp) cc_final: 0.8326 (mpp) REVERT: J 106 LEU cc_start: 0.8895 (mt) cc_final: 0.8620 (mt) REVERT: K 27 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6762 (pp30) REVERT: K 35 TRP cc_start: 0.6732 (m100) cc_final: 0.6232 (m100) REVERT: K 54 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8113 (ttp-170) REVERT: K 61 ARG cc_start: 0.4127 (mtp-110) cc_final: 0.3518 (mtp-110) REVERT: E 95 TYR cc_start: 0.7652 (m-80) cc_final: 0.7182 (m-80) REVERT: F 4 MET cc_start: 0.6680 (mtp) cc_final: 0.6131 (mtp) REVERT: F 46 LEU cc_start: 0.7842 (tp) cc_final: 0.7197 (mp) outliers start: 58 outliers final: 33 residues processed: 335 average time/residue: 0.1923 time to fit residues: 102.8263 Evaluate side-chains 313 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain B residue 192 PHE 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 720 THR Chi-restraints excluded: chain B residue 982 ASP 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 855 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL 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 71 PHE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 27 GLN 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 Chi-restraints excluded: chain F residue 37 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 343 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 147 optimal weight: 0.1980 chunk 250 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 246 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1085 HIS H 59 ASN H 67 HIS L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 37 GLN K 79 GLN E 27 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.151278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093443 restraints weight = 70099.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092922 restraints weight = 46702.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.094213 restraints weight = 34312.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094684 restraints weight = 24958.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094941 restraints weight = 23730.364| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29128 Z= 0.179 Angle : 0.584 10.019 39772 Z= 0.296 Chirality : 0.044 0.240 4629 Planarity : 0.004 0.056 5043 Dihedral : 5.056 50.029 4757 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 2.65 % Allowed : 11.23 % Favored : 86.12 % 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 aren not related in a simple way. whole: 0.38 (0.14), residues: 3531 helix: 2.31 (0.20), residues: 659 sheet: 0.20 (0.17), residues: 881 loop : -0.40 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.023 0.001 TYR H 60 PHE 0.030 0.001 PHE F 71 TRP 0.030 0.002 TRP B 104 HIS 0.004 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00421 (29042) covalent geometry : angle 0.57256 (39557) SS BOND : bond 0.00309 ( 43) SS BOND : angle 1.79442 ( 86) hydrogen bonds : bond 0.03580 ( 1168) hydrogen bonds : angle 5.32270 ( 3180) link_BETA1-4 : bond 0.00413 ( 15) link_BETA1-4 : angle 1.38107 ( 45) link_NAG-ASN : bond 0.00248 ( 28) link_NAG-ASN : angle 1.59325 ( 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 379 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 298 time to evaluate : 0.944 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: A 55 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: A 104 TRP cc_start: 0.7929 (m-90) cc_final: 0.7358 (m-90) REVERT: A 135 PHE cc_start: 0.6518 (p90) cc_final: 0.6175 (p90) REVERT: A 224 GLU cc_start: 0.8782 (pm20) cc_final: 0.8459 (pm20) REVERT: A 266 TYR cc_start: 0.7896 (m-80) cc_final: 0.7423 (m-10) REVERT: A 335 PHE cc_start: 0.9058 (m-10) cc_final: 0.8747 (m-10) REVERT: A 393 TYR cc_start: 0.8910 (m-80) cc_final: 0.8493 (m-80) REVERT: A 449 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9246 (tt) REVERT: A 529 ASN cc_start: 0.8644 (t0) cc_final: 0.8415 (t0) REVERT: A 866 MET cc_start: 0.8505 (mtt) cc_final: 0.8188 (mtt) REVERT: B 202 LYS cc_start: 0.8783 (mttm) cc_final: 0.8442 (mmmm) REVERT: B 271 THR cc_start: 0.9060 (m) cc_final: 0.8449 (p) REVERT: B 295 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: B 348 TYR cc_start: 0.9235 (p90) cc_final: 0.8928 (p90) REVERT: B 352 ARG cc_start: 0.8739 (ttm170) cc_final: 0.8352 (ttt180) REVERT: B 433 TRP cc_start: 0.7231 (p90) cc_final: 0.6760 (p90) REVERT: B 855 LEU cc_start: 0.8364 (mp) cc_final: 0.8021 (mt) REVERT: B 866 MET cc_start: 0.8183 (mtm) cc_final: 0.7717 (ttm) REVERT: B 987 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: B 1026 MET cc_start: 0.8917 (tpp) cc_final: 0.8299 (ttm) REVERT: B 1031 LEU cc_start: 0.9202 (mt) cc_final: 0.8694 (mp) REVERT: C 206 LYS cc_start: 0.8866 (tptt) cc_final: 0.8623 (tptt) REVERT: C 399 ILE cc_start: 0.8069 (pt) cc_final: 0.7752 (pt) REVERT: C 405 ARG cc_start: 0.8411 (ppt170) cc_final: 0.7924 (ppt170) REVERT: C 433 TRP cc_start: 0.8220 (p90) cc_final: 0.7176 (p90) REVERT: C 581 ILE cc_start: 0.8448 (mm) cc_final: 0.7854 (mm) REVERT: C 728 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8941 (ptp) REVERT: C 734 ASP cc_start: 0.7433 (t0) cc_final: 0.7228 (t0) REVERT: C 855 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8899 (mt) REVERT: C 1001 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9302 (tt) REVERT: H 38 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8221 (ttt-90) REVERT: H 64 PHE cc_start: 0.8081 (m-80) cc_final: 0.7855 (m-80) REVERT: L 3 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9240 (tm-30) REVERT: L 4 MET cc_start: 0.8922 (mmm) cc_final: 0.8185 (mmm) REVERT: L 45 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8281 (mmm160) REVERT: J 80 TYR cc_start: 0.8835 (m-80) cc_final: 0.8400 (t80) REVERT: J 106 LEU cc_start: 0.8880 (mt) cc_final: 0.8535 (mt) REVERT: K 24 ARG cc_start: 0.9119 (mtm-85) cc_final: 0.8845 (mpp-170) REVERT: K 27 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6465 (pp30) REVERT: K 54 ARG cc_start: 0.8366 (mtt180) cc_final: 0.8091 (ttp-110) REVERT: E 95 TYR cc_start: 0.7647 (m-80) cc_final: 0.7087 (m-80) REVERT: F 4 MET cc_start: 0.6201 (mtp) cc_final: 0.5679 (mtp) outliers start: 81 outliers final: 48 residues processed: 351 average time/residue: 0.1760 time to fit residues: 98.7157 Evaluate side-chains 328 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 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 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 1062 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1116 ASN 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 566 ILE Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS 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 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 38 ARG Chi-restraints excluded: chain H residue 67 HIS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 27 GLN 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: 20.0000 chunk 137 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 308 optimal weight: 50.0000 chunk 338 optimal weight: 0.0670 chunk 217 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 74 optimal weight: 0.8980 chunk 300 optimal weight: 30.0000 chunk 177 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN E 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.150855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091685 restraints weight = 69404.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093403 restraints weight = 42136.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094264 restraints weight = 25573.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094986 restraints weight = 19677.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095044 restraints weight = 19039.094| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29128 Z= 0.165 Angle : 0.572 12.576 39772 Z= 0.289 Chirality : 0.044 0.236 4629 Planarity : 0.004 0.056 5043 Dihedral : 4.959 51.119 4756 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 12.11 % Favored : 85.63 % 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 aren not related in a simple way. whole: 0.39 (0.14), residues: 3531 helix: 2.44 (0.20), residues: 646 sheet: 0.20 (0.17), residues: 886 loop : -0.42 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 354 TYR 0.024 0.001 TYR C 492 PHE 0.022 0.001 PHE F 71 TRP 0.022 0.001 TRP C 350 HIS 0.019 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00387 (29042) covalent geometry : angle 0.56428 (39557) SS BOND : bond 0.00426 ( 43) SS BOND : angle 1.46725 ( 86) hydrogen bonds : bond 0.03508 ( 1168) hydrogen bonds : angle 5.27480 ( 3180) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.20393 ( 45) link_NAG-ASN : bond 0.00258 ( 28) link_NAG-ASN : angle 1.50330 ( 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 342 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 273 time to evaluate : 1.454 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 55 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7133 (m-10) REVERT: A 104 TRP cc_start: 0.7936 (m-90) cc_final: 0.7410 (m-90) REVERT: A 135 PHE cc_start: 0.6601 (p90) cc_final: 0.6257 (p90) REVERT: A 224 GLU cc_start: 0.8820 (pm20) cc_final: 0.8511 (pm20) REVERT: A 266 TYR cc_start: 0.8020 (m-80) cc_final: 0.7592 (m-10) REVERT: A 323 ILE cc_start: 0.6915 (mt) cc_final: 0.6512 (tt) REVERT: A 335 PHE cc_start: 0.9089 (m-10) cc_final: 0.8785 (m-10) REVERT: A 393 TYR cc_start: 0.9090 (m-80) cc_final: 0.8674 (m-80) REVERT: A 449 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9330 (tt) REVERT: A 494 PHE cc_start: 0.8807 (m-80) cc_final: 0.8266 (m-80) REVERT: A 866 MET cc_start: 0.8482 (mtt) cc_final: 0.8168 (mtt) REVERT: B 202 LYS cc_start: 0.8797 (mttm) cc_final: 0.8435 (mmmm) REVERT: B 271 THR cc_start: 0.9039 (m) cc_final: 0.8411 (p) REVERT: B 295 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: B 314 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: B 348 TYR cc_start: 0.9333 (p90) cc_final: 0.8952 (p90) REVERT: B 433 TRP cc_start: 0.7304 (p90) cc_final: 0.6831 (p90) REVERT: B 853 ASN cc_start: 0.8218 (m-40) cc_final: 0.7827 (t0) REVERT: B 855 LEU cc_start: 0.8317 (mp) cc_final: 0.7929 (mt) REVERT: B 866 MET cc_start: 0.8168 (mtm) cc_final: 0.7736 (ttm) REVERT: B 987 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (tm-30) REVERT: B 1026 MET cc_start: 0.8856 (tpp) cc_final: 0.8249 (ttm) REVERT: B 1031 LEU cc_start: 0.9175 (mt) cc_final: 0.8635 (mp) REVERT: C 206 LYS cc_start: 0.8812 (tptt) cc_final: 0.8611 (tptt) REVERT: C 266 TYR cc_start: 0.7636 (m-80) cc_final: 0.7120 (m-80) REVERT: C 389 PHE cc_start: 0.8151 (m-80) cc_final: 0.7911 (m-80) REVERT: C 399 ILE cc_start: 0.7996 (pt) cc_final: 0.7186 (pt) REVERT: C 405 ARG cc_start: 0.8353 (ppt170) cc_final: 0.7814 (ppt170) REVERT: C 581 ILE cc_start: 0.8443 (mm) cc_final: 0.7837 (mm) REVERT: C 728 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8897 (ptp) REVERT: C 734 ASP cc_start: 0.7483 (t0) cc_final: 0.7031 (t0) REVERT: C 801 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7180 (mt0) REVERT: C 855 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8863 (mt) REVERT: C 1001 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9299 (tt) REVERT: C 1026 MET cc_start: 0.8934 (tpp) cc_final: 0.8329 (ttm) REVERT: H 38 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8639 (ptm-80) REVERT: H 64 PHE cc_start: 0.8369 (m-80) cc_final: 0.7769 (m-80) REVERT: J 80 TYR cc_start: 0.9035 (m-80) cc_final: 0.8642 (t80) REVERT: J 106 LEU cc_start: 0.8990 (mt) cc_final: 0.8663 (mt) REVERT: K 27 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.6200 (pp30) REVERT: K 54 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8272 (ttp-110) REVERT: K 79 GLN cc_start: 0.8293 (mp10) cc_final: 0.7913 (mp10) REVERT: E 95 TYR cc_start: 0.7746 (m-80) cc_final: 0.7238 (m-80) REVERT: F 4 MET cc_start: 0.6701 (mtp) cc_final: 0.6252 (mtp) outliers start: 69 outliers final: 51 residues processed: 317 average time/residue: 0.2033 time to fit residues: 102.2980 Evaluate side-chains 319 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 965 SER 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 295 GLU Chi-restraints excluded: chain B residue 314 ASN 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 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS 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 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 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 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 27 GLN 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: 0.7980 chunk 36 optimal weight: 30.0000 chunk 213 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 335 optimal weight: 40.0000 chunk 312 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 325 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS L 42 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.150369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091989 restraints weight = 69575.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092495 restraints weight = 45541.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092905 restraints weight = 29119.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093572 restraints weight = 25382.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093678 restraints weight = 23369.570| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29128 Z= 0.175 Angle : 0.568 11.582 39772 Z= 0.287 Chirality : 0.043 0.232 4629 Planarity : 0.004 0.057 5043 Dihedral : 4.777 53.903 4754 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.68 % Allowed : 11.98 % Favored : 85.34 % 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 aren not related in a simple way. whole: 0.37 (0.14), residues: 3531 helix: 2.57 (0.20), residues: 634 sheet: 0.20 (0.18), residues: 872 loop : -0.47 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.043 0.002 TYR C 492 PHE 0.016 0.001 PHE B 86 TRP 0.031 0.002 TRP B 104 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00411 (29042) covalent geometry : angle 0.56069 (39557) SS BOND : bond 0.00349 ( 43) SS BOND : angle 1.36056 ( 86) hydrogen bonds : bond 0.03520 ( 1168) hydrogen bonds : angle 5.28975 ( 3180) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.16068 ( 45) link_NAG-ASN : bond 0.00250 ( 28) link_NAG-ASN : angle 1.50984 ( 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 351 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 0.981 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 55 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: A 104 TRP cc_start: 0.7982 (m-90) cc_final: 0.7486 (m-90) REVERT: A 135 PHE cc_start: 0.6503 (p90) cc_final: 0.6125 (p90) REVERT: A 224 GLU cc_start: 0.8854 (pm20) cc_final: 0.8543 (pm20) REVERT: A 266 TYR cc_start: 0.8062 (m-80) cc_final: 0.7746 (m-10) REVERT: A 323 ILE cc_start: 0.7113 (mt) cc_final: 0.6734 (tt) REVERT: A 335 PHE cc_start: 0.9036 (m-10) cc_final: 0.8717 (m-10) REVERT: A 393 TYR cc_start: 0.8935 (m-80) cc_final: 0.8583 (m-80) REVERT: A 448 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5398 (t80) REVERT: A 449 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9296 (tt) REVERT: A 494 PHE cc_start: 0.8703 (m-80) cc_final: 0.8030 (m-80) REVERT: A 866 MET cc_start: 0.8480 (mtt) cc_final: 0.8175 (mtt) REVERT: B 202 LYS cc_start: 0.8804 (mttm) cc_final: 0.8432 (mmmm) REVERT: B 295 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: B 348 TYR cc_start: 0.9276 (p90) cc_final: 0.8949 (p90) REVERT: B 433 TRP cc_start: 0.7311 (p90) cc_final: 0.6735 (p90) REVERT: B 853 ASN cc_start: 0.8170 (m-40) cc_final: 0.7941 (t0) REVERT: B 866 MET cc_start: 0.8161 (mtm) cc_final: 0.7714 (ttm) REVERT: B 1031 LEU cc_start: 0.9189 (mt) cc_final: 0.8674 (mp) REVERT: C 266 TYR cc_start: 0.7635 (m-80) cc_final: 0.7150 (m-80) REVERT: C 405 ARG cc_start: 0.8401 (ppt170) cc_final: 0.7837 (ppt170) REVERT: C 581 ILE cc_start: 0.8454 (mm) cc_final: 0.7860 (mm) REVERT: C 728 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8850 (ptp) REVERT: C 734 ASP cc_start: 0.7475 (t0) cc_final: 0.7099 (t0) REVERT: C 801 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: C 855 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8851 (mt) REVERT: C 1001 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9299 (tt) REVERT: C 1026 MET cc_start: 0.8934 (tpp) cc_final: 0.8354 (ttm) REVERT: H 38 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8524 (ptm-80) REVERT: H 64 PHE cc_start: 0.8357 (m-80) cc_final: 0.8002 (m-80) REVERT: L 44 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: J 80 TYR cc_start: 0.8892 (m-80) cc_final: 0.8514 (t80) REVERT: J 106 LEU cc_start: 0.8937 (mt) cc_final: 0.8674 (mt) REVERT: K 24 ARG cc_start: 0.9137 (mtm-85) cc_final: 0.8876 (mpp-170) REVERT: E 48 MET cc_start: 0.4864 (ppp) cc_final: 0.3849 (pmm) REVERT: E 64 PHE cc_start: 0.8751 (m-80) cc_final: 0.8542 (t80) REVERT: E 95 TYR cc_start: 0.7806 (m-80) cc_final: 0.7233 (m-80) REVERT: F 4 MET cc_start: 0.6492 (mtp) cc_final: 0.6076 (mtp) outliers start: 82 outliers final: 59 residues processed: 322 average time/residue: 0.1670 time to fit residues: 86.0435 Evaluate side-chains 325 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 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 965 SER Chi-restraints excluded: chain A residue 993 LEU 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 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 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 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 945 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 427 THR 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 698 VAL 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 29 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG 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: 5.9990 chunk 273 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 350 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 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** E 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091707 restraints weight = 69644.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093310 restraints weight = 40644.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093827 restraints weight = 27615.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094677 restraints weight = 21452.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094861 restraints weight = 19869.041| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3682 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= 0.154 Angle : 0.561 11.765 39772 Z= 0.283 Chirality : 0.043 0.230 4629 Planarity : 0.004 0.056 5043 Dihedral : 4.667 53.493 4754 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.42 % Allowed : 12.44 % Favored : 85.14 % 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 aren not related in a simple way. whole: 0.40 (0.14), residues: 3531 helix: 2.63 (0.20), residues: 634 sheet: 0.19 (0.17), residues: 890 loop : -0.46 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 45 TYR 0.028 0.001 TYR C 492 PHE 0.022 0.001 PHE A 272 TRP 0.041 0.002 TRP B 104 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00362 (29042) covalent geometry : angle 0.55376 (39557) SS BOND : bond 0.00337 ( 43) SS BOND : angle 1.22446 ( 86) hydrogen bonds : bond 0.03457 ( 1168) hydrogen bonds : angle 5.24033 ( 3180) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.12705 ( 45) link_NAG-ASN : bond 0.00225 ( 28) link_NAG-ASN : angle 1.47251 ( 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 342 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 268 time to evaluate : 1.068 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: 0.7942 (m-90) cc_final: 0.7537 (m-90) REVERT: A 135 PHE cc_start: 0.6558 (p90) cc_final: 0.6186 (p90) REVERT: A 224 GLU cc_start: 0.8866 (pm20) cc_final: 0.8564 (pm20) REVERT: A 266 TYR cc_start: 0.8130 (m-80) cc_final: 0.7854 (m-10) REVERT: A 335 PHE cc_start: 0.9055 (m-10) cc_final: 0.8731 (m-10) REVERT: A 393 TYR cc_start: 0.9012 (m-80) cc_final: 0.8664 (m-80) REVERT: A 448 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.5005 (t80) REVERT: A 449 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9304 (tt) REVERT: A 494 PHE cc_start: 0.8693 (m-80) cc_final: 0.7837 (m-80) REVERT: A 866 MET cc_start: 0.8468 (mtt) cc_final: 0.8178 (mtt) REVERT: A 915 GLU cc_start: 0.8018 (mp0) cc_final: 0.7791 (mp0) REVERT: B 202 LYS cc_start: 0.8769 (mttm) cc_final: 0.8400 (mmmm) REVERT: B 295 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: B 348 TYR cc_start: 0.9306 (p90) cc_final: 0.8961 (p90) REVERT: B 354 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7659 (ttt180) REVERT: B 433 TRP cc_start: 0.7351 (p90) cc_final: 0.6686 (p90) REVERT: B 866 MET cc_start: 0.8246 (mtm) cc_final: 0.7841 (ttm) REVERT: B 1026 MET cc_start: 0.8843 (tpp) cc_final: 0.8026 (ttm) REVERT: C 206 LYS cc_start: 0.8838 (tptt) cc_final: 0.8546 (tptp) REVERT: C 266 TYR cc_start: 0.7696 (m-80) cc_final: 0.7212 (m-80) REVERT: C 405 ARG cc_start: 0.8381 (ppt170) cc_final: 0.7400 (ppt170) REVERT: C 411 GLN cc_start: 0.8514 (tp40) cc_final: 0.7848 (tp40) REVERT: C 581 ILE cc_start: 0.8442 (mm) cc_final: 0.7844 (mm) REVERT: C 728 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8858 (ptp) REVERT: C 734 ASP cc_start: 0.7557 (t0) cc_final: 0.7243 (t0) REVERT: C 801 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7217 (mt0) REVERT: C 855 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8857 (mt) REVERT: C 1001 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9295 (tt) REVERT: C 1026 MET cc_start: 0.8917 (tpp) cc_final: 0.8261 (ttm) REVERT: H 38 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8672 (ptm-80) REVERT: H 64 PHE cc_start: 0.8436 (m-80) cc_final: 0.8029 (m-80) REVERT: L 44 PRO cc_start: 0.8098 (Cg_endo) cc_final: 0.7847 (Cg_exo) REVERT: J 106 LEU cc_start: 0.9011 (mt) cc_final: 0.8757 (mt) REVERT: K 4 MET cc_start: 0.9007 (mmm) cc_final: 0.6910 (mtp) REVERT: E 48 MET cc_start: 0.4844 (ppp) cc_final: 0.3839 (pmm) REVERT: E 64 PHE cc_start: 0.8741 (m-80) cc_final: 0.8512 (t80) REVERT: E 95 TYR cc_start: 0.7855 (m-80) cc_final: 0.7271 (m-80) REVERT: F 4 MET cc_start: 0.6656 (mtp) cc_final: 0.6279 (mtp) outliers start: 74 outliers final: 59 residues processed: 317 average time/residue: 0.1838 time to fit residues: 92.6463 Evaluate side-chains 323 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 965 SER 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 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 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 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 945 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 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 389 PHE 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 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 29 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 35 optimal weight: 0.8980 chunk 351 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 288 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 294 optimal weight: 30.0000 chunk 225 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 ASN ** B 391 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** E 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089534 restraints weight = 69594.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088587 restraints weight = 42886.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088390 restraints weight = 34246.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088810 restraints weight = 32661.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089247 restraints weight = 27082.880| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29128 Z= 0.123 Angle : 0.558 12.026 39772 Z= 0.281 Chirality : 0.043 0.228 4629 Planarity : 0.004 0.058 5043 Dihedral : 4.514 53.420 4754 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.06 % Allowed : 12.90 % Favored : 85.04 % 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 aren not related in a simple way. whole: 0.45 (0.14), residues: 3531 helix: 2.71 (0.21), residues: 638 sheet: 0.22 (0.18), residues: 860 loop : -0.43 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 45 TYR 0.023 0.001 TYR C 492 PHE 0.018 0.001 PHE B 86 TRP 0.026 0.001 TRP C 350 HIS 0.003 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00285 (29042) covalent geometry : angle 0.54891 (39557) SS BOND : bond 0.00290 ( 43) SS BOND : angle 1.63982 ( 86) hydrogen bonds : bond 0.03291 ( 1168) hydrogen bonds : angle 5.14710 ( 3180) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.10107 ( 45) link_NAG-ASN : bond 0.00201 ( 28) link_NAG-ASN : angle 1.40845 ( 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 335 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 272 time to evaluate : 1.088 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: 0.7911 (m-90) cc_final: 0.7557 (m-90) REVERT: A 135 PHE cc_start: 0.6494 (p90) cc_final: 0.6101 (p90) REVERT: A 224 GLU cc_start: 0.8856 (pm20) cc_final: 0.8563 (pm20) REVERT: A 335 PHE cc_start: 0.8959 (m-10) cc_final: 0.8618 (m-10) REVERT: A 393 TYR cc_start: 0.8773 (m-80) cc_final: 0.8503 (m-80) REVERT: A 448 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.3862 (t80) REVERT: A 449 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9267 (tt) REVERT: A 494 PHE cc_start: 0.8544 (m-80) cc_final: 0.7759 (m-80) REVERT: A 866 MET cc_start: 0.8448 (mtt) cc_final: 0.8157 (mtt) REVERT: A 915 GLU cc_start: 0.7969 (mp0) cc_final: 0.7763 (mp0) REVERT: B 202 LYS cc_start: 0.8763 (mttm) cc_final: 0.8380 (mmmm) REVERT: B 295 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: B 348 TYR cc_start: 0.9168 (p90) cc_final: 0.8899 (p90) REVERT: B 354 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7632 (ttt180) REVERT: B 433 TRP cc_start: 0.7200 (p90) cc_final: 0.6588 (p90) REVERT: B 855 LEU cc_start: 0.8184 (mp) cc_final: 0.7878 (mt) REVERT: B 866 MET cc_start: 0.8245 (mtm) cc_final: 0.7832 (ttm) REVERT: B 1026 MET cc_start: 0.8757 (tpp) cc_final: 0.8050 (ttm) REVERT: C 54 LEU cc_start: 0.8346 (mm) cc_final: 0.8141 (tp) REVERT: C 206 LYS cc_start: 0.8754 (tptt) cc_final: 0.8435 (tptp) REVERT: C 266 TYR cc_start: 0.7602 (m-80) cc_final: 0.7260 (m-80) REVERT: C 367 ASN cc_start: 0.8784 (m-40) cc_final: 0.8545 (p0) REVERT: C 405 ARG cc_start: 0.8411 (ppt170) cc_final: 0.7869 (ppt170) REVERT: C 539 ASN cc_start: 0.8822 (t0) cc_final: 0.8583 (t0) REVERT: C 581 ILE cc_start: 0.8456 (mm) cc_final: 0.7861 (mm) REVERT: C 734 ASP cc_start: 0.7461 (t0) cc_final: 0.7094 (t0) REVERT: C 801 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: C 855 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8781 (mt) REVERT: C 1001 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9277 (tt) REVERT: C 1026 MET cc_start: 0.8957 (tpp) cc_final: 0.8383 (ttm) REVERT: H 38 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8490 (ptm-80) REVERT: H 64 PHE cc_start: 0.8266 (m-80) cc_final: 0.7883 (m-80) REVERT: J 80 TYR cc_start: 0.8646 (m-80) cc_final: 0.8264 (t80) REVERT: J 99 HIS cc_start: 0.7743 (t-170) cc_final: 0.7433 (t-170) REVERT: J 106 LEU cc_start: 0.8896 (mt) cc_final: 0.8288 (mt) REVERT: K 24 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8727 (mpp-170) REVERT: E 48 MET cc_start: 0.4722 (ppp) cc_final: 0.3790 (pmm) REVERT: E 95 TYR cc_start: 0.7661 (m-80) cc_final: 0.7124 (m-80) REVERT: E 98 ARG cc_start: 0.5813 (ptt-90) cc_final: 0.4964 (ptt-90) REVERT: F 4 MET cc_start: 0.6400 (mtp) cc_final: 0.6031 (mtp) outliers start: 63 outliers final: 50 residues processed: 312 average time/residue: 0.1742 time to fit residues: 86.8013 Evaluate side-chains 313 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU 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 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 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 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 945 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 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 399 ILE Chi-restraints excluded: chain C residue 427 THR 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 801 GLN 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 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 1 optimal weight: 0.7980 chunk 322 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN ** C 952 ASN ** 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 = 0.4249 r_free = 0.4249 target = 0.145337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089087 restraints weight = 69587.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089633 restraints weight = 43648.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088992 restraints weight = 31752.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089418 restraints weight = 31029.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089794 restraints weight = 26042.934| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29128 Z= 0.115 Angle : 0.554 13.013 39772 Z= 0.278 Chirality : 0.043 0.252 4629 Planarity : 0.004 0.058 5043 Dihedral : 4.397 53.949 4754 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.90 % Allowed : 13.29 % Favored : 84.81 % 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 aren not related in a simple way. whole: 0.48 (0.14), residues: 3531 helix: 2.77 (0.21), residues: 638 sheet: 0.18 (0.18), residues: 868 loop : -0.40 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 61 TYR 0.021 0.001 TYR C 492 PHE 0.036 0.001 PHE A 272 TRP 0.027 0.002 TRP C 350 HIS 0.003 0.001 HIS E 67 Details of bonding type rmsd covalent geometry : bond 0.00265 (29042) covalent geometry : angle 0.54618 (39557) SS BOND : bond 0.00281 ( 43) SS BOND : angle 1.50721 ( 86) hydrogen bonds : bond 0.03193 ( 1168) hydrogen bonds : angle 5.09040 ( 3180) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 1.08585 ( 45) link_NAG-ASN : bond 0.00199 ( 28) link_NAG-ASN : angle 1.38594 ( 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 331 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.997 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: A 104 TRP cc_start: 0.7913 (m-90) cc_final: 0.7564 (m-90) REVERT: A 135 PHE cc_start: 0.6548 (p90) cc_final: 0.6154 (p90) REVERT: A 224 GLU cc_start: 0.8876 (pm20) cc_final: 0.8585 (pm20) REVERT: A 335 PHE cc_start: 0.8975 (m-10) cc_final: 0.8624 (m-10) REVERT: A 393 TYR cc_start: 0.8828 (m-80) cc_final: 0.8551 (m-80) REVERT: A 448 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.3972 (t80) REVERT: A 449 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9280 (tt) REVERT: A 494 PHE cc_start: 0.8570 (m-80) cc_final: 0.7801 (m-80) REVERT: A 866 MET cc_start: 0.8460 (mtt) cc_final: 0.8164 (mtt) REVERT: A 993 LEU cc_start: 0.9066 (mt) cc_final: 0.8837 (mt) REVERT: B 202 LYS cc_start: 0.8766 (mttm) cc_final: 0.8348 (mmmm) REVERT: B 295 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: B 348 TYR cc_start: 0.9180 (p90) cc_final: 0.8924 (p90) REVERT: B 354 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7655 (ttt180) REVERT: B 433 TRP cc_start: 0.7293 (p90) cc_final: 0.6482 (p90) REVERT: B 855 LEU cc_start: 0.8141 (mp) cc_final: 0.7791 (mt) REVERT: B 866 MET cc_start: 0.8213 (mtm) cc_final: 0.7823 (ttm) REVERT: B 1026 MET cc_start: 0.8753 (tpp) cc_final: 0.8051 (ttm) REVERT: C 206 LYS cc_start: 0.8758 (tptt) cc_final: 0.8462 (tptp) REVERT: C 266 TYR cc_start: 0.7570 (m-80) cc_final: 0.7223 (m-80) REVERT: C 367 ASN cc_start: 0.8805 (m-40) cc_final: 0.8562 (p0) REVERT: C 405 ARG cc_start: 0.8391 (ppt170) cc_final: 0.7840 (ppt170) REVERT: C 539 ASN cc_start: 0.8811 (t0) cc_final: 0.8531 (t0) REVERT: C 581 ILE cc_start: 0.8463 (mm) cc_final: 0.7861 (mm) REVERT: C 801 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: C 855 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 1001 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9281 (tt) REVERT: C 1026 MET cc_start: 0.8906 (tpp) cc_final: 0.8309 (ttm) REVERT: H 38 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8413 (ptm-80) REVERT: L 3 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9232 (tm-30) REVERT: J 4 LEU cc_start: 0.7868 (tp) cc_final: 0.7494 (tp) REVERT: J 80 TYR cc_start: 0.8698 (m-80) cc_final: 0.8337 (t80) REVERT: J 99 HIS cc_start: 0.7745 (t-170) cc_final: 0.7396 (t-170) REVERT: J 106 LEU cc_start: 0.8924 (mt) cc_final: 0.8307 (mt) REVERT: K 24 ARG cc_start: 0.9123 (mtm-85) cc_final: 0.8879 (mpp-170) REVERT: E 32 TYR cc_start: 0.6231 (p90) cc_final: 0.6004 (p90) REVERT: E 48 MET cc_start: 0.4775 (ppp) cc_final: 0.3800 (pmm) REVERT: E 95 TYR cc_start: 0.7652 (m-80) cc_final: 0.7130 (m-80) REVERT: F 4 MET cc_start: 0.6492 (mtp) cc_final: 0.6128 (mtp) REVERT: F 46 LEU cc_start: 0.7576 (tp) cc_final: 0.7145 (mt) outliers start: 58 outliers final: 47 residues processed: 311 average time/residue: 0.1709 time to fit residues: 85.3609 Evaluate side-chains 311 residues out of total 3144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU 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 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 1116 ASN 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 315 PHE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 853 ASN 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 36 VAL Chi-restraints excluded: chain C residue 47 VAL 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 698 VAL 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 801 GLN 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 38 ARG Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 118 THR 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: 0.0970 chunk 307 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 243 optimal weight: 0.7980 chunk 331 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 227 optimal weight: 20.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4266 r_free = 0.4266 target = 0.152894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099454 restraints weight = 69930.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097913 restraints weight = 44879.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097530 restraints weight = 36567.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098195 restraints weight = 30608.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098267 restraints weight = 27940.606| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4085 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= 0.120 Angle : 0.566 13.176 39772 Z= 0.284 Chirality : 0.043 0.278 4629 Planarity : 0.004 0.059 5043 Dihedral : 4.357 54.552 4754 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 2.03 % Allowed : 13.42 % Favored : 84.55 % 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 aren not related in a simple way. whole: 0.47 (0.14), residues: 3531 helix: 2.75 (0.21), residues: 638 sheet: 0.15 (0.17), residues: 867 loop : -0.39 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 61 TYR 0.054 0.001 TYR J 110 PHE 0.043 0.001 PHE A 272 TRP 0.041 0.002 TRP C 350 HIS 0.003 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00277 (29042) covalent geometry : angle 0.55872 (39557) SS BOND : bond 0.00306 ( 43) SS BOND : angle 1.39362 ( 86) hydrogen bonds : bond 0.03233 ( 1168) hydrogen bonds : angle 5.08553 ( 3180) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.09561 ( 45) link_NAG-ASN : bond 0.00186 ( 28) link_NAG-ASN : angle 1.34402 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5341.49 seconds wall clock time: 92 minutes 58.90 seconds (5578.90 seconds total)