Starting phenix.real_space_refine on Thu Nov 20 12:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9h_8783/11_2025/5w9h_8783.map" } resolution = 4.0 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= 0.000 sd= 0.004 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 180 5.16 5 C 21408 2.51 5 N 5538 2.21 5 O 6714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33840 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "p" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "q" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "r" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "J" 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: "K" 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: "L" 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: 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: "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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "p" 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: "q" 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: "r" 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 Time building chain proxies: 8.80, per 1000 atoms: 0.26 Number of scatterers: 33840 At special positions: 0 Unit cell: (155.04, 153, 223.38, 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 180 16.00 O 6714 8.00 N 5538 7.00 C 21408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.13 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.05 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.04 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.04 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.21 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.02 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS p 30 " - pdb=" SG CYS p 195 " distance=2.04 Simple disulfide: pdb=" SG CYS p 176 " - pdb=" SG CYS p 214 " distance=2.06 Simple disulfide: pdb=" SG CYS p 185 " - pdb=" SG CYS p 237 " distance=2.09 Simple disulfide: pdb=" SG CYS p 339 " - pdb=" SG CYS p 349 " distance=2.04 Simple disulfide: pdb=" SG CYS p 383 " - pdb=" SG CYS p 407 " distance=2.35 Simple disulfide: pdb=" SG CYS p 425 " - pdb=" SG CYS p 478 " distance=2.02 Simple disulfide: pdb=" SG CYS p 437 " - pdb=" SG CYS p 585 " distance=2.19 Simple disulfide: pdb=" SG CYS p 503 " - pdb=" SG CYS p 526 " distance=2.02 Simple disulfide: pdb=" SG CYS p 603 " - pdb=" SG CYS p 654 " distance=1.85 Simple disulfide: pdb=" SG CYS p 620 " - pdb=" SG CYS p 650 " distance=2.32 Simple disulfide: pdb=" SG CYS p 679 " - pdb=" SG CYS p 713 " distance=2.03 Simple disulfide: pdb=" SG CYS p 727 " - pdb=" SG CYS p 736 " distance=2.08 Simple disulfide: pdb=" SG CYS q 30 " - pdb=" SG CYS q 195 " distance=2.04 Simple disulfide: pdb=" SG CYS q 176 " - pdb=" SG CYS q 214 " distance=2.04 Simple disulfide: pdb=" SG CYS q 185 " - pdb=" SG CYS q 237 " distance=2.03 Simple disulfide: pdb=" SG CYS q 339 " - pdb=" SG CYS q 349 " distance=2.03 Simple disulfide: pdb=" SG CYS q 383 " - pdb=" SG CYS q 407 " distance=2.59 Simple disulfide: pdb=" SG CYS q 425 " - pdb=" SG CYS q 478 " distance=2.14 Simple disulfide: pdb=" SG CYS q 437 " - pdb=" SG CYS q 585 " distance=2.14 Simple disulfide: pdb=" SG CYS q 503 " - pdb=" SG CYS q 526 " distance=2.02 Simple disulfide: pdb=" SG CYS q 603 " - pdb=" SG CYS q 654 " distance=2.05 Simple disulfide: pdb=" SG CYS q 679 " - pdb=" SG CYS q 713 " distance=2.03 Simple disulfide: pdb=" SG CYS q 727 " - pdb=" SG CYS q 736 " distance=2.02 Simple disulfide: pdb=" SG CYS r 30 " - pdb=" SG CYS r 195 " distance=2.05 Simple disulfide: pdb=" SG CYS r 176 " - pdb=" SG CYS r 214 " distance=2.10 Simple disulfide: pdb=" SG CYS r 185 " - pdb=" SG CYS r 237 " distance=2.08 Simple disulfide: pdb=" SG CYS r 339 " - pdb=" SG CYS r 349 " distance=2.04 Simple disulfide: pdb=" SG CYS r 383 " - pdb=" SG CYS r 407 " distance=1.94 Simple disulfide: pdb=" SG CYS r 425 " - pdb=" SG CYS r 478 " distance=2.01 Simple disulfide: pdb=" SG CYS r 437 " - pdb=" SG CYS r 585 " distance=2.06 Simple disulfide: pdb=" SG CYS r 503 " - pdb=" SG CYS r 526 " distance=2.02 Simple disulfide: pdb=" SG CYS r 603 " - pdb=" SG CYS r 654 " distance=2.20 Simple disulfide: pdb=" SG CYS r 620 " - pdb=" SG CYS r 650 " distance=2.13 Simple disulfide: pdb=" SG CYS r 679 " - pdb=" SG CYS r 713 " distance=2.03 Simple disulfide: pdb=" SG CYS r 727 " - pdb=" SG CYS r 736 " distance=2.02 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=1, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG D1401 " - " ASN D 774 " " NAG G1401 " - " ASN G 774 " " NAG J 1 " - " ASN A1176 " " NAG K 1 " - " ASN A1213 " " NAG L 1 " - " ASN A 785 " " NAG M 1 " - " ASN A 870 " " NAG N 1 " - " ASN D 785 " " NAG O 1 " - " ASN D1213 " " NAG P 1 " - " ASN D 870 " " NAG Q 1 " - " ASN D1176 " " NAG R 1 " - " ASN G 785 " " NAG S 1 " - " ASN G1176 " " NAG T 1 " - " ASN G 870 " " NAG U 1 " - " ASN G1213 " " NAG V 1 " - " ASN p 244 " " NAG W 1 " - " ASN p 66 " " NAG X 1 " - " ASN p 125 " " NAG Y 1 " - " ASN q 66 " " NAG Z 1 " - " ASN q 125 " " NAG a 1 " - " ASN q 244 " " NAG b 1 " - " ASN r 125 " " NAG c 1 " - " ASN r 66 " " NAG d 1 " - " ASN r 244 " " NAG p1401 " - " ASN p 236 " " NAG p1402 " - " ASN p 104 " " NAG p1403 " - " ASN p 166 " " NAG p1404 " - " ASN p 155 " " NAG p1405 " - " ASN p 719 " " NAG p1406 " - " ASN p 619 " " NAG q1401 " - " ASN q 166 " " NAG q1402 " - " ASN q 236 " " NAG q1403 " - " ASN q 619 " " NAG q1404 " - " ASN q 719 " " NAG q1405 " - " ASN q 104 " " NAG q1406 " - " ASN q 155 " " NAG r1401 " - " ASN r 719 " " NAG r1402 " - " ASN r 104 " " NAG r1403 " - " ASN r 166 " " NAG r1404 " - " ASN r 155 " " NAG r1405 " - " ASN r 619 " " NAG r1406 " - " ASN r 236 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7902 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 75 sheets defined 23.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.158A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.883A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.724A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 954 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.545A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.852A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 822 removed outlier: 3.740A pdb=" N ARG D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.791A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 4.670A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1039 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 4.075A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.652A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.883A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 908 through 912 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.600A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.553A pdb=" N LEU G1033 " --> pdb=" O ASN G1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.257A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'p' and resid 37 through 41 Processing helix chain 'p' and resid 49 through 53 Processing helix chain 'p' and resid 104 through 108 Processing helix chain 'p' and resid 133 through 137 Processing helix chain 'p' and resid 222 through 230 Processing helix chain 'p' and resid 303 through 307 removed outlier: 3.789A pdb=" N ARG p 307 " --> pdb=" O GLN p 304 " (cutoff:3.500A) Processing helix chain 'p' and resid 342 through 351 Processing helix chain 'p' and resid 385 through 390 removed outlier: 3.510A pdb=" N SER p 390 " --> pdb=" O PRO p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 395 through 399 removed outlier: 3.656A pdb=" N PHE p 399 " --> pdb=" O VAL p 396 " (cutoff:3.500A) Processing helix chain 'p' and resid 410 through 415 Processing helix chain 'p' and resid 416 through 418 No H-bonds generated for 'chain 'p' and resid 416 through 418' Processing helix chain 'p' and resid 429 through 436 removed outlier: 3.898A pdb=" N ALA p 434 " --> pdb=" O PRO p 430 " (cutoff:3.500A) Processing helix chain 'p' and resid 449 through 456 removed outlier: 4.839A pdb=" N SER p 454 " --> pdb=" O SER p 451 " (cutoff:3.500A) Processing helix chain 'p' and resid 462 through 468 Processing helix chain 'p' and resid 524 through 529 Processing helix chain 'p' and resid 546 through 550 Processing helix chain 'p' and resid 675 through 678 removed outlier: 3.597A pdb=" N ALA p 678 " --> pdb=" O GLY p 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 675 through 678' Processing helix chain 'p' and resid 694 through 702 removed outlier: 3.569A pdb=" N LYS p 698 " --> pdb=" O ARG p 694 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG p 700 " --> pdb=" O MET p 696 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 41 removed outlier: 4.150A pdb=" N ASP q 41 " --> pdb=" O THR q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 49 through 53 Processing helix chain 'q' and resid 104 through 108 Processing helix chain 'q' and resid 133 through 137 Processing helix chain 'q' and resid 222 through 230 Processing helix chain 'q' and resid 303 through 307 removed outlier: 3.945A pdb=" N ARG q 307 " --> pdb=" O GLN q 304 " (cutoff:3.500A) Processing helix chain 'q' and resid 342 through 351 Processing helix chain 'q' and resid 385 through 390 removed outlier: 3.630A pdb=" N SER q 390 " --> pdb=" O PRO q 387 " (cutoff:3.500A) Processing helix chain 'q' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU q 414 " --> pdb=" O ASN q 410 " (cutoff:3.500A) Processing helix chain 'q' and resid 431 through 436 Processing helix chain 'q' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER q 454 " --> pdb=" O SER q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 462 through 468 Processing helix chain 'q' and resid 524 through 529 Processing helix chain 'q' and resid 676 through 678 No H-bonds generated for 'chain 'q' and resid 676 through 678' Processing helix chain 'q' and resid 694 through 702 removed outlier: 3.630A pdb=" N LYS q 698 " --> pdb=" O ARG q 694 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG q 700 " --> pdb=" O MET q 696 " (cutoff:3.500A) Processing helix chain 'r' and resid 37 through 41 Processing helix chain 'r' and resid 49 through 53 Processing helix chain 'r' and resid 104 through 108 Processing helix chain 'r' and resid 133 through 137 Processing helix chain 'r' and resid 222 through 230 Processing helix chain 'r' and resid 268 through 273 removed outlier: 4.130A pdb=" N LEU r 273 " --> pdb=" O ARG r 269 " (cutoff:3.500A) Processing helix chain 'r' and resid 303 through 307 removed outlier: 3.852A pdb=" N ARG r 307 " --> pdb=" O GLN r 304 " (cutoff:3.500A) Processing helix chain 'r' and resid 342 through 351 Processing helix chain 'r' and resid 385 through 389 Processing helix chain 'r' and resid 410 through 416 removed outlier: 4.007A pdb=" N LEU r 414 " --> pdb=" O ASN r 410 " (cutoff:3.500A) Processing helix chain 'r' and resid 429 through 436 Processing helix chain 'r' and resid 449 through 456 removed outlier: 4.518A pdb=" N SER r 454 " --> pdb=" O SER r 451 " (cutoff:3.500A) Processing helix chain 'r' and resid 462 through 468 Processing helix chain 'r' and resid 524 through 529 Processing helix chain 'r' and resid 546 through 550 Processing helix chain 'r' and resid 675 through 678 removed outlier: 3.542A pdb=" N ALA r 678 " --> pdb=" O GLY r 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 675 through 678' Processing helix chain 'r' and resid 694 through 702 removed outlier: 3.602A pdb=" N LYS r 698 " --> pdb=" O ARG r 694 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG r 700 " --> pdb=" O MET r 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'p' and resid 719 through 724 removed outlier: 7.313A pdb=" N LEU A 759 " --> pdb=" O SER p 720 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU p 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.693A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 6.030A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.498A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.498A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.495A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.913A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'q' and resid 719 through 724 removed outlier: 7.307A pdb=" N LEU D 759 " --> pdb=" O SER q 720 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU q 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.632A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.942A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.329A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.270A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.270A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.173A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'r' and resid 719 through 724 removed outlier: 7.265A pdb=" N LEU G 759 " --> pdb=" O SER r 720 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU r 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY r 732 " --> pdb=" O LEU r 735 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA r 737 " --> pdb=" O PRO r 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.962A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 3.605A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.319A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 96 through 99 removed outlier: 5.350A pdb=" N TYR H 97 " --> pdb=" O ALA H 100D" (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA H 100D" --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL H 99 " --> pdb=" O VAL H 100B" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.718A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'p' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'p' and resid 68 through 75 removed outlier: 3.690A pdb=" N ARG p 335 " --> pdb=" O ASP p 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'p' and resid 83 through 85 removed outlier: 6.415A pdb=" N SER p 267 " --> pdb=" O GLN p 280 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN p 280 " --> pdb=" O SER p 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'p' and resid 88 through 89 removed outlier: 7.534A pdb=" N SER p 88 " --> pdb=" O ILE p 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'p' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'p' and resid 110 through 111 removed outlier: 4.432A pdb=" N ALA p 146 " --> pdb=" O ILE p 296 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU p 180 " --> pdb=" O THR p 242 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR p 242 " --> pdb=" O LEU p 180 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA p 182 " --> pdb=" O MET p 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET p 240 " --> pdb=" O ALA p 182 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR p 184 " --> pdb=" O THR p 238 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE p 186 " --> pdb=" O ASN p 236 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN p 236 " --> pdb=" O ILE p 186 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU p 188 " --> pdb=" O LEU p 234 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU p 234 " --> pdb=" O GLU p 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'p' and resid 126 through 127 removed outlier: 4.612A pdb=" N SER p 126 " --> pdb=" O ILE p 140 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA p 309 " --> pdb=" O THR p 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'p' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'p' and resid 359 through 366 removed outlier: 4.314A pdb=" N VAL p 659 " --> pdb=" O VAL p 363 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER p 365 " --> pdb=" O VAL p 657 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL p 657 " --> pdb=" O SER p 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'p' and resid 371 through 376 removed outlier: 4.656A pdb=" N GLU p 605 " --> pdb=" O GLY p 372 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL p 604 " --> pdb=" O GLY p 615 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY p 615 " --> pdb=" O VAL p 604 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'p' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR p 483 " --> pdb=" O VAL p 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL p 420 " --> pdb=" O THR p 483 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'p' and resid 513 through 515 removed outlier: 5.400A pdb=" N SER p 498 " --> pdb=" O VAL p 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL p 561 " --> pdb=" O SER p 498 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE p 500 " --> pdb=" O SER p 559 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER p 559 " --> pdb=" O ILE p 500 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'p' and resid 617 through 619 removed outlier: 4.907A pdb=" N VAL p 639 " --> pdb=" O LEU p 651 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL p 631 " --> pdb=" O VAL p 639 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'q' and resid 33 through 35 Processing sheet with id=AF3, first strand: chain 'q' and resid 68 through 72 removed outlier: 3.670A pdb=" N ARG q 335 " --> pdb=" O ASP q 326 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'q' and resid 75 through 76 Processing sheet with id=AF5, first strand: chain 'q' and resid 75 through 76 removed outlier: 6.509A pdb=" N SER q 267 " --> pdb=" O GLN q 280 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN q 280 " --> pdb=" O SER q 267 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'q' and resid 88 through 89 removed outlier: 7.572A pdb=" N SER q 88 " --> pdb=" O ILE q 300 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'q' and resid 92 through 93 Processing sheet with id=AF8, first strand: chain 'q' and resid 110 through 111 removed outlier: 4.462A pdb=" N ALA q 146 " --> pdb=" O ILE q 296 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS q 185 " --> pdb=" O THR q 168 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU q 180 " --> pdb=" O THR q 242 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR q 242 " --> pdb=" O LEU q 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA q 182 " --> pdb=" O MET q 240 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET q 240 " --> pdb=" O ALA q 182 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR q 184 " --> pdb=" O THR q 238 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE q 186 " --> pdb=" O ASN q 236 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN q 236 " --> pdb=" O ILE q 186 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU q 188 " --> pdb=" O LEU q 234 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU q 234 " --> pdb=" O GLU q 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'q' and resid 126 through 127 removed outlier: 4.435A pdb=" N SER q 126 " --> pdb=" O ILE q 140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA q 309 " --> pdb=" O THR q 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'q' and resid 153 through 154 Processing sheet with id=AG2, first strand: chain 'q' and resid 359 through 366 removed outlier: 4.164A pdb=" N VAL q 659 " --> pdb=" O VAL q 363 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER q 365 " --> pdb=" O VAL q 657 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL q 657 " --> pdb=" O SER q 365 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY q 675 " --> pdb=" O PRO q 658 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N CYS q 713 " --> pdb=" O PHE q 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 374 through 375 Processing sheet with id=AG4, first strand: chain 'q' and resid 381 through 382 removed outlier: 6.120A pdb=" N VAL q 381 " --> pdb=" O ASN q 408 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N CYS q 407 " --> pdb=" O CYS q 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'q' and resid 400 through 404 removed outlier: 3.565A pdb=" N LYS q 400 " --> pdb=" O TYR q 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR q 483 " --> pdb=" O VAL q 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL q 420 " --> pdb=" O THR q 483 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER q 498 " --> pdb=" O VAL q 561 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL q 561 " --> pdb=" O SER q 498 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE q 500 " --> pdb=" O SER q 559 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER q 559 " --> pdb=" O ILE q 500 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'q' and resid 617 through 619 removed outlier: 5.244A pdb=" N VAL q 639 " --> pdb=" O LEU q 651 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL q 631 " --> pdb=" O VAL q 639 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'r' and resid 33 through 35 Processing sheet with id=AG9, first strand: chain 'r' and resid 68 through 72 removed outlier: 3.709A pdb=" N ARG r 335 " --> pdb=" O ASP r 326 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'r' and resid 83 through 85 removed outlier: 6.434A pdb=" N SER r 267 " --> pdb=" O GLN r 280 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN r 280 " --> pdb=" O SER r 267 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'r' and resid 88 through 89 removed outlier: 7.505A pdb=" N SER r 88 " --> pdb=" O ILE r 300 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 92 through 93 Processing sheet with id=AH4, first strand: chain 'r' and resid 110 through 111 removed outlier: 4.502A pdb=" N ALA r 146 " --> pdb=" O ILE r 296 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU r 180 " --> pdb=" O THR r 242 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR r 242 " --> pdb=" O LEU r 180 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA r 182 " --> pdb=" O MET r 240 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET r 240 " --> pdb=" O ALA r 182 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR r 184 " --> pdb=" O THR r 238 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE r 186 " --> pdb=" O ASN r 236 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN r 236 " --> pdb=" O ILE r 186 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'r' and resid 126 through 127 removed outlier: 4.356A pdb=" N SER r 126 " --> pdb=" O ILE r 140 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA r 309 " --> pdb=" O THR r 139 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'r' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'r' and resid 359 through 366 removed outlier: 4.397A pdb=" N VAL r 659 " --> pdb=" O VAL r 363 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER r 365 " --> pdb=" O VAL r 657 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL r 657 " --> pdb=" O SER r 365 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'r' and resid 371 through 375 removed outlier: 7.404A pdb=" N SER r 371 " --> pdb=" O GLU r 605 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER r 607 " --> pdb=" O SER r 371 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N SER r 373 " --> pdb=" O SER r 607 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'r' and resid 381 through 382 removed outlier: 6.416A pdb=" N VAL r 381 " --> pdb=" O ASN r 408 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N CYS r 407 " --> pdb=" O CYS r 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'r' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS r 400 " --> pdb=" O TYR r 445 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR r 483 " --> pdb=" O VAL r 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL r 420 " --> pdb=" O THR r 483 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'r' and resid 513 through 515 removed outlier: 5.436A pdb=" N SER r 498 " --> pdb=" O VAL r 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL r 561 " --> pdb=" O SER r 498 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE r 500 " --> pdb=" O SER r 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER r 559 " --> pdb=" O ILE r 500 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'r' and resid 617 through 620 removed outlier: 4.428A pdb=" N TYR r 648 " --> pdb=" O CYS r 620 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL r 639 " --> pdb=" O LEU r 651 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL r 631 " --> pdb=" O VAL r 639 " (cutoff:3.500A) 1266 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6079 1.32 - 1.46: 12659 1.46 - 1.60: 15632 1.60 - 1.74: 1 1.74 - 1.88: 246 Bond restraints: 34617 Sorted by residual: bond pdb=" CA VAL r 584 " pdb=" C VAL r 584 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.23e-02 6.61e+03 5.22e+01 bond pdb=" CA CYS p 437 " pdb=" C CYS p 437 " ideal model delta sigma weight residual 1.523 1.608 -0.085 1.30e-02 5.92e+03 4.26e+01 bond pdb=" N CYS p 185 " pdb=" CA CYS p 185 " ideal model delta sigma weight residual 1.455 1.530 -0.075 1.25e-02 6.40e+03 3.60e+01 bond pdb=" C CYS r 437 " pdb=" O CYS r 437 " ideal model delta sigma weight residual 1.235 1.301 -0.067 1.18e-02 7.18e+03 3.19e+01 bond pdb=" C1 NAG D1401 " pdb=" O5 NAG D1401 " ideal model delta sigma weight residual 1.406 1.515 -0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 34612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 45137 3.87 - 7.74: 1784 7.74 - 11.62: 138 11.62 - 15.49: 12 15.49 - 19.36: 2 Bond angle restraints: 47073 Sorted by residual: angle pdb=" N GLN r 688 " pdb=" CA GLN r 688 " pdb=" C GLN r 688 " ideal model delta sigma weight residual 111.28 123.29 -12.01 1.09e+00 8.42e-01 1.22e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.00 -7.34 7.20e-01 1.93e+00 1.04e+02 angle pdb=" C THR G 961 " pdb=" N ALA G 962 " pdb=" CA ALA G 962 " ideal model delta sigma weight residual 121.54 140.90 -19.36 1.91e+00 2.74e-01 1.03e+02 angle pdb=" C LEU q 284 " pdb=" N PRO q 285 " pdb=" CA PRO q 285 " ideal model delta sigma weight residual 119.56 129.26 -9.70 1.01e+00 9.80e-01 9.21e+01 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.55 -6.89 7.20e-01 1.93e+00 9.15e+01 ... (remaining 47068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 20723 23.68 - 47.36: 489 47.36 - 71.04: 195 71.04 - 94.72: 28 94.72 - 118.40: 24 Dihedral angle restraints: 21459 sinusoidal: 9069 harmonic: 12390 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 170.28 -77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 168.03 -75.03 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.41 -74.41 1 1.00e+01 1.00e-02 7.02e+01 ... (remaining 21456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 5377 0.296 - 0.591: 20 0.591 - 0.887: 5 0.887 - 1.182: 3 1.182 - 1.478: 1 Chirality restraints: 5406 Sorted by residual: chirality pdb=" C1 NAG p1402 " pdb=" ND2 ASN p 104 " pdb=" C2 NAG p1402 " pdb=" O5 NAG p1402 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-01 2.50e+01 5.46e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN r 66 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN G 870 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 5403 not shown) Planarity restraints: 6066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN q 166 " -0.172 2.00e-02 2.50e+03 1.81e-01 4.11e+02 pdb=" CG ASN q 166 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN q 166 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN q 166 " 0.264 2.00e-02 2.50e+03 pdb=" C1 NAG q1401 " -0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D1213 " 0.045 2.00e-02 2.50e+03 5.22e-02 3.41e+01 pdb=" CG ASN D1213 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN D1213 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D1213 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 806 " 0.026 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" C CYS D 806 " -0.089 2.00e-02 2.50e+03 pdb=" O CYS D 806 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 807 " 0.030 2.00e-02 2.50e+03 ... (remaining 6063 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 16 2.05 - 2.76: 6813 2.76 - 3.47: 46170 3.47 - 4.19: 83460 4.19 - 4.90: 138558 Nonbonded interactions: 275017 Sorted by model distance: nonbonded pdb=" OH TYR D 905 " pdb=" CA PRO D 936 " model vdw 1.336 3.470 nonbonded pdb=" CD1 LEU D 773 " pdb=" O TYR D 777 " model vdw 1.441 3.460 nonbonded pdb=" OH TYR G 905 " pdb=" O VAL G 934 " model vdw 1.486 3.040 nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.506 3.470 nonbonded pdb=" OH TYR A 905 " pdb=" CB PRO A 936 " model vdw 1.514 3.440 ... (remaining 275012 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'p' selection = chain 'q' selection = chain 'r' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.050 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.561 34737 Z= 0.877 Angle : 1.801 38.176 47374 Z= 1.163 Chirality : 0.090 1.478 5406 Planarity : 0.011 0.104 6024 Dihedral : 12.297 118.402 13389 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.62 % Favored : 95.77 % Rotamer: Outliers : 0.16 % Allowed : 0.74 % Favored : 99.10 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.13), residues: 4227 helix: -0.42 (0.16), residues: 688 sheet: 0.94 (0.15), residues: 948 loop : 1.86 (0.13), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG p 652 TYR 0.057 0.006 TYR q 469 PHE 0.030 0.004 PHE I 32 TRP 0.059 0.007 TRP H 47 HIS 0.007 0.002 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.01348 (34617) covalent geometry : angle 1.70362 (47073) SS BOND : bond 0.11026 ( 56) SS BOND : angle 6.80442 ( 112) hydrogen bonds : bond 0.19413 ( 1252) hydrogen bonds : angle 8.22885 ( 3228) Misc. bond : bond 0.14995 ( 1) link_BETA1-4 : bond 0.01317 ( 21) link_BETA1-4 : angle 5.38855 ( 63) link_NAG-ASN : bond 0.01926 ( 42) link_NAG-ASN : angle 8.95277 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 791 time to evaluate : 1.347 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 877 VAL cc_start: 0.6917 (t) cc_final: 0.5742 (p) REVERT: A 924 ILE cc_start: 0.6273 (mt) cc_final: 0.5933 (pt) REVERT: A 1105 GLU cc_start: 0.7898 (tt0) cc_final: 0.7363 (tt0) REVERT: B 28 THR cc_start: 0.9338 (m) cc_final: 0.9032 (p) REVERT: B 45 LEU cc_start: 0.8562 (mp) cc_final: 0.8329 (mp) REVERT: D 816 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8199 (tptm) REVERT: D 911 ASP cc_start: 0.7791 (m-30) cc_final: 0.7366 (t0) REVERT: D 927 GLN cc_start: 0.8410 (tt0) cc_final: 0.7898 (tt0) REVERT: D 1097 GLN cc_start: 0.8253 (tp40) cc_final: 0.7688 (tm-30) REVERT: D 1101 ASP cc_start: 0.8313 (m-30) cc_final: 0.7988 (m-30) REVERT: D 1222 LEU cc_start: 0.9080 (tp) cc_final: 0.8760 (pt) REVERT: E 51 PHE cc_start: 0.8261 (t80) cc_final: 0.7793 (t80) REVERT: E 82 LEU cc_start: 0.7052 (tt) cc_final: 0.6652 (tt) REVERT: F 33 MET cc_start: 0.8734 (tpp) cc_final: 0.8359 (tpp) REVERT: F 73 LEU cc_start: 0.8178 (tp) cc_final: 0.7242 (tp) REVERT: G 913 MET cc_start: 0.6240 (ttt) cc_final: 0.6025 (ttt) REVERT: G 938 LEU cc_start: 0.9344 (tp) cc_final: 0.8717 (tp) REVERT: G 939 MET cc_start: 0.7259 (mtp) cc_final: 0.6369 (mtp) REVERT: G 1079 ASN cc_start: 0.8834 (m-40) cc_final: 0.8299 (t0) REVERT: p 147 PHE cc_start: 0.8250 (m-80) cc_final: 0.7323 (m-80) REVERT: p 347 LEU cc_start: 0.9271 (tp) cc_final: 0.8991 (tt) REVERT: p 523 TYR cc_start: 0.6091 (m-80) cc_final: 0.5843 (m-80) REVERT: q 563 MET cc_start: 0.6688 (ptt) cc_final: 0.6211 (tpt) REVERT: q 728 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7620 (tptt) REVERT: r 54 ASP cc_start: 0.8379 (m-30) cc_final: 0.7984 (m-30) REVERT: r 218 ASN cc_start: 0.8822 (t0) cc_final: 0.8508 (p0) REVERT: r 278 MET cc_start: 0.8992 (mmm) cc_final: 0.8485 (mmp) REVERT: r 356 VAL cc_start: 0.9062 (t) cc_final: 0.8798 (t) REVERT: r 401 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6857 (mmt90) REVERT: r 402 LEU cc_start: 0.7926 (mt) cc_final: 0.7639 (mp) REVERT: r 436 ASN cc_start: 0.7818 (m-40) cc_final: 0.7573 (t0) REVERT: r 445 TYR cc_start: 0.5082 (p90) cc_final: 0.4823 (p90) REVERT: r 505 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7451 (ptm160) REVERT: r 587 LYS cc_start: 0.6801 (tttt) cc_final: 0.6455 (pttt) REVERT: r 592 ASN cc_start: 0.7337 (m-40) cc_final: 0.6962 (p0) REVERT: r 663 TYR cc_start: 0.8754 (t80) cc_final: 0.8319 (t80) REVERT: r 664 ASP cc_start: 0.7490 (t0) cc_final: 0.7120 (t0) outliers start: 6 outliers final: 1 residues processed: 795 average time/residue: 0.2370 time to fit residues: 299.5778 Evaluate side-chains 357 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 629 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN B 1 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1208 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 89 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN G 836 HIS G1104 ASN G1132 ASN G1217 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN H 61 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 261 GLN q 107 GLN q 377 GLN r 280 GLN ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.097282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072379 restraints weight = 148905.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074577 restraints weight = 76787.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.076007 restraints weight = 50839.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.076877 restraints weight = 39238.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077382 restraints weight = 33523.848| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34737 Z= 0.204 Angle : 0.867 14.904 47374 Z= 0.441 Chirality : 0.052 0.462 5406 Planarity : 0.007 0.095 6024 Dihedral : 10.345 109.501 5956 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.26 % Rotamer: Outliers : 2.30 % Allowed : 8.18 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.13), residues: 4227 helix: 0.95 (0.19), residues: 698 sheet: 0.62 (0.15), residues: 1051 loop : 0.97 (0.13), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG r 141 TYR 0.038 0.002 TYR A 905 PHE 0.027 0.002 PHE r 385 TRP 0.023 0.002 TRP F 35 HIS 0.007 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00434 (34617) covalent geometry : angle 0.81865 (47073) SS BOND : bond 0.00537 ( 56) SS BOND : angle 2.06291 ( 112) hydrogen bonds : bond 0.06553 ( 1252) hydrogen bonds : angle 6.52587 ( 3228) Misc. bond : bond 0.00918 ( 1) link_BETA1-4 : bond 0.00560 ( 21) link_BETA1-4 : angle 3.48374 ( 63) link_NAG-ASN : bond 0.00813 ( 42) link_NAG-ASN : angle 4.73611 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 439 time to evaluate : 1.428 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 924 ILE cc_start: 0.6602 (mt) cc_final: 0.6165 (pt) REVERT: A 967 PHE cc_start: 0.8245 (t80) cc_final: 0.7937 (t80) REVERT: B 45 LEU cc_start: 0.8732 (mp) cc_final: 0.8382 (mt) REVERT: B 46 GLU cc_start: 0.8656 (pt0) cc_final: 0.8095 (pm20) REVERT: C 33 MET cc_start: 0.8725 (tpp) cc_final: 0.8362 (tpp) REVERT: C 75 ILE cc_start: 0.9098 (mt) cc_final: 0.8885 (mm) REVERT: C 92 LYS cc_start: 0.9276 (tptm) cc_final: 0.8785 (ttmt) REVERT: D 816 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8302 (tptt) REVERT: D 843 ASP cc_start: 0.8468 (m-30) cc_final: 0.8053 (t0) REVERT: D 927 GLN cc_start: 0.8249 (tt0) cc_final: 0.7122 (pt0) REVERT: D 933 LYS cc_start: 0.8156 (mttt) cc_final: 0.7795 (mttt) REVERT: D 1078 LEU cc_start: 0.9270 (mt) cc_final: 0.8807 (tp) REVERT: D 1097 GLN cc_start: 0.8479 (tp40) cc_final: 0.7814 (tm-30) REVERT: D 1101 ASP cc_start: 0.8397 (m-30) cc_final: 0.7978 (m-30) REVERT: D 1222 LEU cc_start: 0.9028 (tp) cc_final: 0.8746 (pt) REVERT: E 51 PHE cc_start: 0.8173 (t80) cc_final: 0.7633 (t80) REVERT: E 61 GLN cc_start: 0.7311 (tp40) cc_final: 0.7090 (tp40) REVERT: F 33 MET cc_start: 0.8888 (tpp) cc_final: 0.8675 (tpp) REVERT: F 73 LEU cc_start: 0.8381 (tp) cc_final: 0.7899 (tp) REVERT: F 86 TYR cc_start: 0.7764 (m-80) cc_final: 0.7546 (m-80) REVERT: G 909 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5862 (t80) REVERT: G 1104 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8701 (t0) REVERT: H 38 LYS cc_start: 0.8110 (tttm) cc_final: 0.7815 (ttmm) REVERT: H 59 TYR cc_start: 0.7889 (m-10) cc_final: 0.7354 (m-10) REVERT: I 38 GLN cc_start: 0.8048 (tt0) cc_final: 0.7411 (tt0) REVERT: p 147 PHE cc_start: 0.8148 (m-80) cc_final: 0.7768 (m-80) REVERT: p 330 ASP cc_start: 0.8237 (p0) cc_final: 0.8015 (p0) REVERT: p 332 TYR cc_start: 0.8521 (m-80) cc_final: 0.8260 (m-80) REVERT: p 563 MET cc_start: 0.3719 (ptp) cc_final: 0.2885 (tpp) REVERT: p 696 MET cc_start: 0.3229 (ptm) cc_final: 0.2900 (ppp) REVERT: q 148 MET cc_start: 0.8344 (ttt) cc_final: 0.8140 (ttt) REVERT: q 149 LEU cc_start: 0.8966 (mm) cc_final: 0.8719 (mm) REVERT: q 563 MET cc_start: 0.6765 (ptt) cc_final: 0.6126 (tpt) REVERT: q 728 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7764 (tptt) REVERT: q 729 LEU cc_start: 0.9028 (mt) cc_final: 0.8777 (mp) REVERT: r 388 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.5967 (mt) REVERT: r 436 ASN cc_start: 0.7800 (m-40) cc_final: 0.7503 (t0) REVERT: r 505 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7538 (ptm160) REVERT: r 663 TYR cc_start: 0.8759 (t80) cc_final: 0.8554 (t80) outliers start: 84 outliers final: 45 residues processed: 499 average time/residue: 0.2197 time to fit residues: 180.7849 Evaluate side-chains 371 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1078 LEU Chi-restraints excluded: chain G residue 1104 ASN Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 445 TYR Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 676 SER Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 225 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 386 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1104 ASN A1212 GLN B 1 GLN B 58 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 90 GLN D 857 GLN D 927 GLN D1056 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 89 GLN G 772 GLN G1063 GLN G1104 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 38 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 280 GLN p 421 ASN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 GLN q 107 GLN ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 475 ASN ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 98 GLN ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 637 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071323 restraints weight = 149814.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.074607 restraints weight = 82002.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.074722 restraints weight = 46278.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075032 restraints weight = 39691.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.075164 restraints weight = 38298.871| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34737 Z= 0.221 Angle : 0.808 13.609 47374 Z= 0.405 Chirality : 0.051 0.548 5406 Planarity : 0.006 0.084 6024 Dihedral : 9.596 105.583 5952 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 10.04 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4227 helix: 1.06 (0.20), residues: 692 sheet: 0.52 (0.15), residues: 1029 loop : 0.41 (0.13), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 887 TYR 0.030 0.002 TYR A 905 PHE 0.023 0.002 PHE I 98 TRP 0.029 0.002 TRP F 35 HIS 0.008 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00485 (34617) covalent geometry : angle 0.76550 (47073) SS BOND : bond 0.00683 ( 56) SS BOND : angle 1.62713 ( 112) hydrogen bonds : bond 0.05686 ( 1252) hydrogen bonds : angle 6.20963 ( 3228) Misc. bond : bond 0.01042 ( 1) link_BETA1-4 : bond 0.00628 ( 21) link_BETA1-4 : angle 3.36152 ( 63) link_NAG-ASN : bond 0.00710 ( 42) link_NAG-ASN : angle 4.27944 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 358 time to evaluate : 1.383 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: A 757 MET cc_start: 0.8226 (mtp) cc_final: 0.7955 (mmp) REVERT: A 967 PHE cc_start: 0.8354 (t80) cc_final: 0.8018 (t80) REVERT: B 45 LEU cc_start: 0.8677 (mp) cc_final: 0.8448 (mp) REVERT: C 27 GLU cc_start: 0.7944 (pt0) cc_final: 0.7701 (pm20) REVERT: C 32 PHE cc_start: 0.7887 (m-80) cc_final: 0.7632 (m-10) REVERT: C 90 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8011 (pp30) REVERT: C 92 LYS cc_start: 0.9430 (tptm) cc_final: 0.8980 (tppp) REVERT: D 816 LYS cc_start: 0.8442 (mmmt) cc_final: 0.7978 (tptm) REVERT: D 843 ASP cc_start: 0.8406 (m-30) cc_final: 0.7848 (t0) REVERT: D 927 GLN cc_start: 0.8408 (tt0) cc_final: 0.8163 (tt0) REVERT: D 938 LEU cc_start: 0.8985 (tp) cc_final: 0.8367 (tp) REVERT: D 1097 GLN cc_start: 0.8561 (tp40) cc_final: 0.8323 (tm-30) REVERT: D 1222 LEU cc_start: 0.8952 (tp) cc_final: 0.8687 (pt) REVERT: F 33 MET cc_start: 0.8840 (tpp) cc_final: 0.8607 (tpp) REVERT: F 38 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: F 73 LEU cc_start: 0.8401 (tp) cc_final: 0.7950 (tp) REVERT: F 87 PHE cc_start: 0.8561 (m-80) cc_final: 0.8173 (m-80) REVERT: F 89 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: G 906 MET cc_start: 0.5884 (mmt) cc_final: 0.5677 (mmt) REVERT: G 909 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6208 (t80) REVERT: G 1180 ILE cc_start: 0.9269 (mp) cc_final: 0.8775 (tt) REVERT: H 39 GLN cc_start: 0.8198 (tt0) cc_final: 0.7698 (tt0) REVERT: H 59 TYR cc_start: 0.7946 (m-10) cc_final: 0.7370 (m-10) REVERT: H 81 GLU cc_start: 0.8487 (tt0) cc_final: 0.7761 (tp30) REVERT: H 85 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8204 (mp0) REVERT: I 89 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7791 (tm-30) REVERT: p 147 PHE cc_start: 0.8317 (m-80) cc_final: 0.7908 (m-80) REVERT: p 563 MET cc_start: 0.3661 (ptp) cc_final: 0.2720 (tpp) REVERT: q 148 MET cc_start: 0.8497 (ttt) cc_final: 0.7772 (ttt) REVERT: q 149 LEU cc_start: 0.9017 (mm) cc_final: 0.8689 (mt) REVERT: q 324 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8906 (mm) REVERT: q 563 MET cc_start: 0.6861 (ptt) cc_final: 0.6137 (tpt) REVERT: q 637 ASN cc_start: 0.8236 (t0) cc_final: 0.7979 (t0) REVERT: q 728 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7811 (tptt) REVERT: r 436 ASN cc_start: 0.7967 (m-40) cc_final: 0.7519 (t0) REVERT: r 505 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7452 (ptm160) REVERT: r 663 TYR cc_start: 0.8751 (t80) cc_final: 0.8529 (t80) outliers start: 91 outliers final: 65 residues processed: 427 average time/residue: 0.2087 time to fit residues: 149.8872 Evaluate side-chains 376 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 828 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 909 TYR Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1151 SER Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 324 LEU Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 367 GLU Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 459 SER Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 676 SER Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 413 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 304 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 987 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 1 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** D 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D1110 GLN D1212 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN G1217 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 398 ASN q 521 ASN ** q 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 107 GLN ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 468 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.095717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071863 restraints weight = 149754.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074814 restraints weight = 82360.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075078 restraints weight = 49356.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075565 restraints weight = 39975.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075656 restraints weight = 37811.818| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34737 Z= 0.159 Angle : 0.750 13.200 47374 Z= 0.368 Chirality : 0.050 0.631 5406 Planarity : 0.005 0.074 6024 Dihedral : 8.863 105.359 5952 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.05 % Favored : 95.72 % Rotamer: Outliers : 2.60 % Allowed : 10.78 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 4227 helix: 1.13 (0.20), residues: 710 sheet: 0.53 (0.15), residues: 1070 loop : 0.15 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 822 TYR 0.027 0.001 TYR A 905 PHE 0.024 0.001 PHE B 63 TRP 0.035 0.002 TRP F 35 HIS 0.007 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00341 (34617) covalent geometry : angle 0.70915 (47073) SS BOND : bond 0.00401 ( 56) SS BOND : angle 1.34521 ( 112) hydrogen bonds : bond 0.05037 ( 1252) hydrogen bonds : angle 5.87316 ( 3228) Misc. bond : bond 0.01585 ( 1) link_BETA1-4 : bond 0.00622 ( 21) link_BETA1-4 : angle 3.19634 ( 63) link_NAG-ASN : bond 0.00715 ( 42) link_NAG-ASN : angle 4.10439 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 356 time to evaluate : 1.446 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: A 1063 GLN cc_start: 0.8952 (tt0) cc_final: 0.8561 (tt0) REVERT: C 22 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (p) REVERT: C 27 GLU cc_start: 0.7982 (pt0) cc_final: 0.7763 (pm20) REVERT: C 32 PHE cc_start: 0.8005 (m-80) cc_final: 0.7749 (m-10) REVERT: C 42 GLN cc_start: 0.9043 (pt0) cc_final: 0.8563 (pm20) REVERT: C 74 ASN cc_start: 0.8837 (p0) cc_final: 0.8223 (t0) REVERT: C 92 LYS cc_start: 0.9361 (tptm) cc_final: 0.8830 (tppp) REVERT: C 93 GLU cc_start: 0.8622 (pm20) cc_final: 0.8379 (pm20) REVERT: D 927 GLN cc_start: 0.8414 (tt0) cc_final: 0.8170 (tt0) REVERT: D 1222 LEU cc_start: 0.8948 (tp) cc_final: 0.8673 (pt) REVERT: E 61 GLN cc_start: 0.7469 (tp40) cc_final: 0.7197 (tp40) REVERT: F 15 LEU cc_start: 0.8002 (tp) cc_final: 0.7455 (mp) REVERT: F 27 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8319 (tm-30) REVERT: F 33 MET cc_start: 0.8793 (tpp) cc_final: 0.8548 (tpp) REVERT: F 87 PHE cc_start: 0.8485 (m-80) cc_final: 0.8149 (m-80) REVERT: F 89 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: G 757 MET cc_start: 0.8254 (mmt) cc_final: 0.7900 (mmp) REVERT: G 1180 ILE cc_start: 0.9236 (mp) cc_final: 0.8740 (tt) REVERT: H 39 GLN cc_start: 0.8331 (tt0) cc_final: 0.7745 (tt0) REVERT: H 81 GLU cc_start: 0.8589 (tt0) cc_final: 0.7836 (tp30) REVERT: H 85 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8261 (mp0) REVERT: I 33 MET cc_start: 0.8635 (tpp) cc_final: 0.8418 (tpt) REVERT: I 104 LEU cc_start: 0.7910 (tp) cc_final: 0.7703 (tt) REVERT: p 278 MET cc_start: 0.7683 (tpp) cc_final: 0.7387 (tpp) REVERT: p 330 ASP cc_start: 0.8414 (p0) cc_final: 0.8207 (p0) REVERT: p 332 TYR cc_start: 0.8664 (m-80) cc_final: 0.8209 (m-80) REVERT: p 563 MET cc_start: 0.3486 (ptp) cc_final: 0.2251 (tpp) REVERT: q 148 MET cc_start: 0.8586 (ttt) cc_final: 0.8164 (ttt) REVERT: q 427 GLN cc_start: 0.6937 (mt0) cc_final: 0.6655 (mt0) REVERT: q 468 ASN cc_start: 0.4237 (m-40) cc_final: 0.3055 (m-40) REVERT: q 637 ASN cc_start: 0.8237 (t0) cc_final: 0.7930 (t0) REVERT: q 728 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7844 (tptt) REVERT: r 183 PHE cc_start: 0.7041 (m-80) cc_final: 0.5655 (m-80) REVERT: r 346 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: r 436 ASN cc_start: 0.8096 (m-40) cc_final: 0.7570 (t0) REVERT: r 505 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7424 (ptm160) REVERT: r 663 TYR cc_start: 0.8682 (t80) cc_final: 0.8460 (t80) outliers start: 95 outliers final: 59 residues processed: 426 average time/residue: 0.2013 time to fit residues: 146.4016 Evaluate side-chains 370 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 1 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1181 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain p residue 734 SER Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 445 TYR Chi-restraints excluded: chain q residue 472 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 173 optimal weight: 3.9990 chunk 324 optimal weight: 40.0000 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 409 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 249 optimal weight: 40.0000 chunk 301 optimal weight: 30.0000 chunk 182 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 ASN A1146 HIS B 39 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 819 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 833 GLN G1217 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN p 98 GLN p 167 HIS ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 60 GLN ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.092699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067985 restraints weight = 148629.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070772 restraints weight = 83532.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071151 restraints weight = 48644.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071584 restraints weight = 40721.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071654 restraints weight = 38777.807| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34737 Z= 0.247 Angle : 0.801 13.178 47374 Z= 0.398 Chirality : 0.050 0.465 5406 Planarity : 0.006 0.074 6024 Dihedral : 8.594 103.373 5952 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.96 % Rotamer: Outliers : 3.17 % Allowed : 11.74 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4227 helix: 0.94 (0.19), residues: 704 sheet: 0.26 (0.15), residues: 1056 loop : -0.14 (0.13), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 887 TYR 0.030 0.002 TYR A 905 PHE 0.021 0.002 PHE F 32 TRP 0.044 0.002 TRP F 35 HIS 0.007 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00547 (34617) covalent geometry : angle 0.76516 (47073) SS BOND : bond 0.00469 ( 56) SS BOND : angle 1.45405 ( 112) hydrogen bonds : bond 0.05254 ( 1252) hydrogen bonds : angle 5.98827 ( 3228) Misc. bond : bond 0.02477 ( 1) link_BETA1-4 : bond 0.00613 ( 21) link_BETA1-4 : angle 3.28447 ( 63) link_NAG-ASN : bond 0.00635 ( 42) link_NAG-ASN : angle 3.89332 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 330 time to evaluate : 1.390 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: A 842 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8287 (tp40) REVERT: B 100 MET cc_start: 0.7922 (mmt) cc_final: 0.7612 (mmm) REVERT: C 90 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: C 92 LYS cc_start: 0.9465 (tptm) cc_final: 0.8998 (tppp) REVERT: C 93 GLU cc_start: 0.8826 (pm20) cc_final: 0.8557 (pm20) REVERT: D 843 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7944 (t70) REVERT: D 927 GLN cc_start: 0.8601 (tt0) cc_final: 0.8343 (tt0) REVERT: D 1222 LEU cc_start: 0.8970 (tp) cc_final: 0.8714 (pt) REVERT: F 4 LEU cc_start: 0.7929 (mt) cc_final: 0.7649 (mm) REVERT: F 27 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8452 (tm-30) REVERT: F 33 MET cc_start: 0.8902 (tpp) cc_final: 0.8681 (tpp) REVERT: F 38 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: F 73 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8060 (tp) REVERT: F 87 PHE cc_start: 0.8452 (m-80) cc_final: 0.8051 (m-80) REVERT: F 93 GLU cc_start: 0.8402 (pm20) cc_final: 0.7699 (pm20) REVERT: G 1105 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: G 1180 ILE cc_start: 0.9137 (mp) cc_final: 0.8651 (tt) REVERT: H 39 GLN cc_start: 0.8427 (tt0) cc_final: 0.8222 (tt0) REVERT: H 81 GLU cc_start: 0.8608 (tt0) cc_final: 0.7818 (tp30) REVERT: H 85 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8258 (mp0) REVERT: I 17 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8296 (mt0) REVERT: I 33 MET cc_start: 0.8664 (tpp) cc_final: 0.8433 (tpt) REVERT: I 90 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (pp30) REVERT: p 147 PHE cc_start: 0.8466 (m-80) cc_final: 0.8092 (m-80) REVERT: p 278 MET cc_start: 0.7786 (tpp) cc_final: 0.7523 (tpp) REVERT: p 330 ASP cc_start: 0.8500 (p0) cc_final: 0.8282 (p0) REVERT: p 563 MET cc_start: 0.3360 (ptp) cc_final: 0.2132 (tpp) REVERT: q 148 MET cc_start: 0.8529 (ttt) cc_final: 0.8164 (ttt) REVERT: q 468 ASN cc_start: 0.4104 (m-40) cc_final: 0.3005 (m-40) REVERT: q 637 ASN cc_start: 0.8422 (t0) cc_final: 0.8064 (t0) REVERT: q 728 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7860 (tptt) REVERT: r 204 PHE cc_start: 0.8163 (t80) cc_final: 0.7949 (t80) REVERT: r 240 MET cc_start: 0.8109 (tpt) cc_final: 0.7650 (tpp) REVERT: r 346 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: r 505 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7492 (ptm160) REVERT: r 592 ASN cc_start: 0.7559 (m-40) cc_final: 0.7066 (p0) REVERT: r 663 TYR cc_start: 0.8794 (t80) cc_final: 0.8555 (t80) outliers start: 116 outliers final: 82 residues processed: 414 average time/residue: 0.1959 time to fit residues: 137.0985 Evaluate side-chains 383 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 294 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1105 GLU Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1151 SER Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 717 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 554 LEU Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 399 optimal weight: 50.0000 chunk 29 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 316 optimal weight: 30.0000 chunk 108 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 247 optimal weight: 0.0980 chunk 151 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1217 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 468 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.094075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069276 restraints weight = 145806.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072255 restraints weight = 82382.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072543 restraints weight = 46667.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072992 restraints weight = 39889.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073058 restraints weight = 37648.365| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34737 Z= 0.156 Angle : 0.734 13.447 47374 Z= 0.361 Chirality : 0.049 0.429 5406 Planarity : 0.005 0.070 6024 Dihedral : 8.306 104.031 5952 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.57 % Favored : 95.22 % Rotamer: Outliers : 2.68 % Allowed : 12.92 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4227 helix: 1.06 (0.20), residues: 716 sheet: 0.38 (0.15), residues: 1052 loop : -0.22 (0.13), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 699 TYR 0.037 0.001 TYR D 777 PHE 0.024 0.001 PHE C 32 TRP 0.023 0.001 TRP F 35 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00341 (34617) covalent geometry : angle 0.69719 (47073) SS BOND : bond 0.00634 ( 56) SS BOND : angle 1.64002 ( 112) hydrogen bonds : bond 0.04813 ( 1252) hydrogen bonds : angle 5.70760 ( 3228) Misc. bond : bond 0.00664 ( 1) link_BETA1-4 : bond 0.00629 ( 21) link_BETA1-4 : angle 3.14133 ( 63) link_NAG-ASN : bond 0.00599 ( 42) link_NAG-ASN : angle 3.70175 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 329 time to evaluate : 1.399 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: A 782 ILE cc_start: 0.9156 (mt) cc_final: 0.8885 (mt) REVERT: A 842 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8301 (tp40) REVERT: B 100 MET cc_start: 0.7957 (mmt) cc_final: 0.7667 (mmm) REVERT: C 42 GLN cc_start: 0.9009 (pt0) cc_final: 0.8565 (pm20) REVERT: C 87 PHE cc_start: 0.9148 (m-80) cc_final: 0.8945 (m-80) REVERT: C 90 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: C 92 LYS cc_start: 0.9457 (tptm) cc_final: 0.9124 (tppp) REVERT: D 843 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7781 (t70) REVERT: D 927 GLN cc_start: 0.8525 (tt0) cc_final: 0.8216 (tt0) REVERT: D 1222 LEU cc_start: 0.8948 (tp) cc_final: 0.8742 (pt) REVERT: F 4 LEU cc_start: 0.8002 (mt) cc_final: 0.7700 (mm) REVERT: F 15 LEU cc_start: 0.8099 (tp) cc_final: 0.7534 (mp) REVERT: F 27 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8352 (tm-30) REVERT: F 87 PHE cc_start: 0.8443 (m-80) cc_final: 0.8105 (m-80) REVERT: F 90 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6866 (pp30) REVERT: F 93 GLU cc_start: 0.8353 (pm20) cc_final: 0.7719 (pm20) REVERT: G 1180 ILE cc_start: 0.9099 (mp) cc_final: 0.8612 (tt) REVERT: H 39 GLN cc_start: 0.8389 (tt0) cc_final: 0.7321 (tt0) REVERT: H 81 GLU cc_start: 0.8633 (tt0) cc_final: 0.7881 (tp30) REVERT: H 85 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8282 (mp0) REVERT: I 17 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8329 (mt0) REVERT: I 33 MET cc_start: 0.8645 (tpp) cc_final: 0.8416 (tpt) REVERT: p 147 PHE cc_start: 0.8336 (m-80) cc_final: 0.7914 (m-80) REVERT: p 278 MET cc_start: 0.7749 (tpp) cc_final: 0.7538 (tpp) REVERT: p 330 ASP cc_start: 0.8427 (p0) cc_final: 0.8210 (p0) REVERT: p 563 MET cc_start: 0.3380 (ptp) cc_final: 0.2017 (tpp) REVERT: q 148 MET cc_start: 0.8427 (ttt) cc_final: 0.8130 (ttt) REVERT: q 278 MET cc_start: 0.8368 (mpp) cc_final: 0.8017 (mmm) REVERT: q 468 ASN cc_start: 0.3978 (m-40) cc_final: 0.3167 (m-40) REVERT: q 637 ASN cc_start: 0.8451 (t0) cc_final: 0.8061 (t0) REVERT: q 728 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7912 (tptt) REVERT: r 240 MET cc_start: 0.8022 (tpt) cc_final: 0.7685 (tpp) REVERT: r 346 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: r 592 ASN cc_start: 0.7479 (m-40) cc_final: 0.7194 (t0) REVERT: r 663 TYR cc_start: 0.8781 (t80) cc_final: 0.8534 (t80) outliers start: 98 outliers final: 82 residues processed: 400 average time/residue: 0.1956 time to fit residues: 131.2439 Evaluate side-chains 391 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 305 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1063 GLN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 119 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 GLN ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 GLN p 516 GLN p 637 ASN ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 194 HIS ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 421 ASN r 733 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.091629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067497 restraints weight = 149505.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069379 restraints weight = 85135.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069941 restraints weight = 55181.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070336 restraints weight = 46534.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070380 restraints weight = 45115.633| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 34737 Z= 0.265 Angle : 0.812 13.120 47374 Z= 0.404 Chirality : 0.050 0.439 5406 Planarity : 0.005 0.078 6024 Dihedral : 8.377 100.145 5952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.91 % Favored : 93.87 % Rotamer: Outliers : 3.26 % Allowed : 13.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4227 helix: 0.74 (0.19), residues: 714 sheet: 0.11 (0.15), residues: 1074 loop : -0.51 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG r 542 TYR 0.042 0.002 TYR D 777 PHE 0.019 0.002 PHE I 98 TRP 0.020 0.002 TRP F 35 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00588 (34617) covalent geometry : angle 0.77787 (47073) SS BOND : bond 0.00566 ( 56) SS BOND : angle 1.68393 ( 112) hydrogen bonds : bond 0.05220 ( 1252) hydrogen bonds : angle 5.95254 ( 3228) Misc. bond : bond 0.02951 ( 1) link_BETA1-4 : bond 0.00637 ( 21) link_BETA1-4 : angle 3.23413 ( 63) link_NAG-ASN : bond 0.00607 ( 42) link_NAG-ASN : angle 3.73835 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 308 time to evaluate : 1.508 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: A 1063 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: B 39 GLN cc_start: 0.9078 (tp40) cc_final: 0.8685 (tp40) REVERT: C 74 ASN cc_start: 0.9103 (p0) cc_final: 0.8491 (t0) REVERT: D 843 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7728 (t0) REVERT: D 857 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: D 927 GLN cc_start: 0.8608 (tt0) cc_final: 0.8337 (tt0) REVERT: D 1222 LEU cc_start: 0.8987 (tp) cc_final: 0.8767 (pt) REVERT: E 28 THR cc_start: 0.7465 (p) cc_final: 0.7144 (t) REVERT: F 4 LEU cc_start: 0.8019 (mt) cc_final: 0.7712 (mm) REVERT: F 27 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8325 (tm-30) REVERT: F 87 PHE cc_start: 0.8512 (m-80) cc_final: 0.8128 (m-80) REVERT: H 39 GLN cc_start: 0.8446 (tt0) cc_final: 0.8194 (tt0) REVERT: H 69 MET cc_start: 0.7416 (mtp) cc_final: 0.6995 (mtm) REVERT: H 81 GLU cc_start: 0.8614 (tt0) cc_final: 0.7812 (tp30) REVERT: H 85 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8339 (mp0) REVERT: p 147 PHE cc_start: 0.8495 (m-80) cc_final: 0.8177 (m-80) REVERT: p 278 MET cc_start: 0.7868 (tpp) cc_final: 0.7622 (tpp) REVERT: p 563 MET cc_start: 0.3461 (ptp) cc_final: 0.2090 (tpp) REVERT: q 148 MET cc_start: 0.8470 (ttt) cc_final: 0.8209 (ttt) REVERT: q 278 MET cc_start: 0.8622 (mpp) cc_final: 0.8120 (mmm) REVERT: q 468 ASN cc_start: 0.4061 (m-40) cc_final: 0.3030 (m-40) REVERT: q 637 ASN cc_start: 0.8583 (t0) cc_final: 0.8185 (t0) REVERT: q 686 MET cc_start: 0.4995 (mmm) cc_final: 0.4693 (mmm) REVERT: q 728 LYS cc_start: 0.8443 (mmtt) cc_final: 0.7890 (tptt) REVERT: r 204 PHE cc_start: 0.8145 (t80) cc_final: 0.7929 (t80) REVERT: r 346 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8805 (tm-30) REVERT: r 592 ASN cc_start: 0.7659 (m-40) cc_final: 0.7082 (p0) REVERT: r 663 TYR cc_start: 0.8823 (t80) cc_final: 0.8612 (t80) outliers start: 119 outliers final: 89 residues processed: 393 average time/residue: 0.2000 time to fit residues: 131.9056 Evaluate side-chains 384 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 291 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1063 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1181 VAL Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 629 ARG Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 36 GLN Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 561 VAL Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 255 optimal weight: 50.0000 chunk 392 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 313 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.098753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077754 restraints weight = 165068.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078917 restraints weight = 107277.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079122 restraints weight = 75035.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079110 restraints weight = 71627.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079241 restraints weight = 69098.705| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34737 Z= 0.251 Angle : 0.805 13.411 47374 Z= 0.399 Chirality : 0.050 0.435 5406 Planarity : 0.005 0.069 6024 Dihedral : 8.367 101.572 5952 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.77 % Favored : 94.01 % Rotamer: Outliers : 3.15 % Allowed : 13.44 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4227 helix: 0.66 (0.19), residues: 714 sheet: 0.03 (0.15), residues: 1064 loop : -0.66 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 61 TYR 0.033 0.002 TYR D 777 PHE 0.020 0.002 PHE C 98 TRP 0.041 0.002 TRP r 553 HIS 0.006 0.002 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00557 (34617) covalent geometry : angle 0.77129 (47073) SS BOND : bond 0.00528 ( 56) SS BOND : angle 1.60408 ( 112) hydrogen bonds : bond 0.05182 ( 1252) hydrogen bonds : angle 5.90659 ( 3228) Misc. bond : bond 0.00545 ( 1) link_BETA1-4 : bond 0.00625 ( 21) link_BETA1-4 : angle 3.20365 ( 63) link_NAG-ASN : bond 0.00588 ( 42) link_NAG-ASN : angle 3.72734 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 299 time to evaluate : 1.403 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: B 39 GLN cc_start: 0.9168 (tp40) cc_final: 0.8712 (tp40) REVERT: C 42 GLN cc_start: 0.8971 (pt0) cc_final: 0.8534 (pm20) REVERT: C 92 LYS cc_start: 0.9416 (tptm) cc_final: 0.8838 (tptm) REVERT: D 843 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7802 (t0) REVERT: D 857 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8423 (mp10) REVERT: D 927 GLN cc_start: 0.8582 (tt0) cc_final: 0.8311 (tt0) REVERT: E 28 THR cc_start: 0.7611 (p) cc_final: 0.7313 (t) REVERT: F 4 LEU cc_start: 0.8077 (mt) cc_final: 0.7822 (mm) REVERT: F 33 MET cc_start: 0.8751 (tpp) cc_final: 0.6941 (ptt) REVERT: F 38 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: F 87 PHE cc_start: 0.8482 (m-80) cc_final: 0.8181 (m-80) REVERT: G 757 MET cc_start: 0.8485 (mmt) cc_final: 0.8213 (mmt) REVERT: G 1105 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: G 1119 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: H 39 GLN cc_start: 0.8535 (tt0) cc_final: 0.8325 (tt0) REVERT: H 59 TYR cc_start: 0.8302 (m-10) cc_final: 0.7832 (m-10) REVERT: H 69 MET cc_start: 0.7422 (mtp) cc_final: 0.7047 (mtm) REVERT: H 81 GLU cc_start: 0.8554 (tt0) cc_final: 0.8274 (mp0) REVERT: H 85 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8346 (mp0) REVERT: p 147 PHE cc_start: 0.8409 (m-80) cc_final: 0.8106 (m-80) REVERT: p 278 MET cc_start: 0.7876 (tpp) cc_final: 0.7583 (tpp) REVERT: p 563 MET cc_start: 0.3557 (ptp) cc_final: 0.2200 (tpp) REVERT: q 148 MET cc_start: 0.8540 (ttt) cc_final: 0.8296 (ttt) REVERT: q 278 MET cc_start: 0.8706 (mpp) cc_final: 0.8330 (mmm) REVERT: q 428 ILE cc_start: 0.8130 (tt) cc_final: 0.7915 (tt) REVERT: q 468 ASN cc_start: 0.4202 (m-40) cc_final: 0.3221 (m-40) REVERT: q 637 ASN cc_start: 0.8610 (t0) cc_final: 0.8210 (t0) REVERT: q 728 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7963 (tptt) REVERT: r 346 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8826 (tm-30) REVERT: r 563 MET cc_start: 0.5512 (tpp) cc_final: 0.3298 (ppp) REVERT: r 663 TYR cc_start: 0.8815 (t80) cc_final: 0.8564 (t80) outliers start: 115 outliers final: 94 residues processed: 385 average time/residue: 0.2031 time to fit residues: 132.9054 Evaluate side-chains 383 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1008 MET Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1078 LEU Chi-restraints excluded: chain D residue 1181 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1189 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 829 SER Chi-restraints excluded: chain G residue 935 LEU Chi-restraints excluded: chain G residue 1005 LEU Chi-restraints excluded: chain G residue 1036 LEU Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1105 GLU Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1119 GLN Chi-restraints excluded: chain G residue 1127 VAL Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1214 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 148 MET Chi-restraints excluded: chain p residue 206 THR Chi-restraints excluded: chain p residue 265 LEU Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 600 LEU Chi-restraints excluded: chain p residue 629 ARG Chi-restraints excluded: chain q residue 49 ASP Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 424 THR Chi-restraints excluded: chain q residue 426 SER Chi-restraints excluded: chain q residue 537 ASP Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain q residue 735 LEU Chi-restraints excluded: chain r residue 36 GLN Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 171 LEU Chi-restraints excluded: chain r residue 183 PHE Chi-restraints excluded: chain r residue 251 LEU Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 233 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 402 optimal weight: 7.9990 chunk 405 optimal weight: 0.8980 chunk 397 optimal weight: 0.1980 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 0.0070 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 167 HIS r 377 GLN ** r 468 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.093638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069097 restraints weight = 145895.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072090 restraints weight = 80280.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072313 restraints weight = 48984.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072799 restraints weight = 38793.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072917 restraints weight = 38098.852| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34737 Z= 0.131 Angle : 0.733 13.737 47374 Z= 0.359 Chirality : 0.048 0.468 5406 Planarity : 0.005 0.067 6024 Dihedral : 7.911 101.684 5952 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.02 % Favored : 94.77 % Rotamer: Outliers : 2.24 % Allowed : 14.70 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4227 helix: 1.18 (0.20), residues: 698 sheet: 0.19 (0.15), residues: 1083 loop : -0.49 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 979 TYR 0.033 0.001 TYR D 777 PHE 0.016 0.001 PHE C 62 TRP 0.021 0.001 TRP F 35 HIS 0.006 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00281 (34617) covalent geometry : angle 0.69878 (47073) SS BOND : bond 0.00452 ( 56) SS BOND : angle 1.63022 ( 112) hydrogen bonds : bond 0.04541 ( 1252) hydrogen bonds : angle 5.44943 ( 3228) Misc. bond : bond 0.01705 ( 1) link_BETA1-4 : bond 0.00631 ( 21) link_BETA1-4 : angle 3.05455 ( 63) link_NAG-ASN : bond 0.00624 ( 42) link_NAG-ASN : angle 3.53048 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 332 time to evaluate : 1.466 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: A 842 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8328 (tp40) REVERT: A 891 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 39 GLN cc_start: 0.9191 (tp40) cc_final: 0.8701 (tp-100) REVERT: C 92 LYS cc_start: 0.9364 (tptm) cc_final: 0.8795 (tptm) REVERT: D 843 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7928 (t70) REVERT: D 857 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: D 927 GLN cc_start: 0.8443 (tt0) cc_final: 0.8206 (tt0) REVERT: E 28 THR cc_start: 0.7733 (p) cc_final: 0.7484 (t) REVERT: F 4 LEU cc_start: 0.8109 (mt) cc_final: 0.7815 (mm) REVERT: F 15 LEU cc_start: 0.8075 (tp) cc_final: 0.7547 (mm) REVERT: F 33 MET cc_start: 0.8713 (tpp) cc_final: 0.6922 (ptp) REVERT: F 93 GLU cc_start: 0.8568 (pm20) cc_final: 0.7700 (pm20) REVERT: G 757 MET cc_start: 0.8377 (mmt) cc_final: 0.8139 (mmt) REVERT: G 1119 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: H 39 GLN cc_start: 0.8456 (tt0) cc_final: 0.7852 (tt0) REVERT: H 59 TYR cc_start: 0.8191 (m-10) cc_final: 0.7793 (m-10) REVERT: H 81 GLU cc_start: 0.8609 (tt0) cc_final: 0.8344 (mp0) REVERT: H 85 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8352 (mp0) REVERT: I 92 LYS cc_start: 0.8549 (tttt) cc_final: 0.8325 (tttt) REVERT: p 100 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7311 (mm) REVERT: p 147 PHE cc_start: 0.8335 (m-80) cc_final: 0.8029 (m-80) REVERT: p 330 ASP cc_start: 0.8368 (p0) cc_final: 0.8091 (p0) REVERT: p 563 MET cc_start: 0.3771 (ptp) cc_final: 0.2462 (tpp) REVERT: p 696 MET cc_start: 0.4087 (ppp) cc_final: 0.3113 (ppp) REVERT: q 148 MET cc_start: 0.8429 (ttt) cc_final: 0.8140 (ttt) REVERT: q 278 MET cc_start: 0.8638 (mpp) cc_final: 0.8230 (mmm) REVERT: q 428 ILE cc_start: 0.7787 (tt) cc_final: 0.7571 (tt) REVERT: q 468 ASN cc_start: 0.4096 (m-40) cc_final: 0.3189 (m-40) REVERT: q 637 ASN cc_start: 0.8556 (t0) cc_final: 0.8138 (t0) REVERT: q 728 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7945 (tptt) REVERT: r 204 PHE cc_start: 0.8134 (t80) cc_final: 0.7874 (t80) REVERT: r 346 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: r 388 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.5957 (mt) REVERT: r 563 MET cc_start: 0.5567 (tpp) cc_final: 0.2858 (ppp) REVERT: r 592 ASN cc_start: 0.7597 (m-40) cc_final: 0.7154 (p0) REVERT: r 614 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7759 (ptm160) REVERT: r 663 TYR cc_start: 0.8784 (t80) cc_final: 0.8542 (t80) outliers start: 82 outliers final: 62 residues processed: 394 average time/residue: 0.2073 time to fit residues: 138.3167 Evaluate side-chains 367 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1091 SER Chi-restraints excluded: chain D residue 1181 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1119 GLN Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 727 CYS Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 604 VAL Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 409 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 313 optimal weight: 0.1980 chunk 191 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 291 optimal weight: 0.0870 chunk 78 optimal weight: 0.0970 chunk 206 optimal weight: 7.9990 overall best weight: 2.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN ** r 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068397 restraints weight = 149440.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071439 restraints weight = 82778.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071717 restraints weight = 48626.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071973 restraints weight = 39137.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072161 restraints weight = 39489.823| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34737 Z= 0.154 Angle : 0.746 15.849 47374 Z= 0.365 Chirality : 0.048 0.461 5406 Planarity : 0.005 0.066 6024 Dihedral : 7.769 99.580 5952 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.56 % Favored : 94.20 % Rotamer: Outliers : 1.97 % Allowed : 15.41 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4227 helix: 1.24 (0.20), residues: 698 sheet: 0.21 (0.15), residues: 1082 loop : -0.51 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG p 629 TYR 0.030 0.001 TYR D 777 PHE 0.029 0.001 PHE r 313 TRP 0.051 0.002 TRP F 35 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00345 (34617) covalent geometry : angle 0.71284 (47073) SS BOND : bond 0.00442 ( 56) SS BOND : angle 1.82235 ( 112) hydrogen bonds : bond 0.04543 ( 1252) hydrogen bonds : angle 5.44325 ( 3228) Misc. bond : bond 0.00423 ( 1) link_BETA1-4 : bond 0.00629 ( 21) link_BETA1-4 : angle 3.00770 ( 63) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 3.48498 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 1.461 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: A 842 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8404 (tp40) REVERT: A 891 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6922 (mt-10) REVERT: A 1104 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8308 (t0) REVERT: B 39 GLN cc_start: 0.9165 (tp40) cc_final: 0.8713 (tp-100) REVERT: C 92 LYS cc_start: 0.9365 (tptm) cc_final: 0.8829 (tptm) REVERT: D 843 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7746 (t0) REVERT: D 857 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: D 927 GLN cc_start: 0.8480 (tt0) cc_final: 0.8245 (tt0) REVERT: E 28 THR cc_start: 0.7646 (p) cc_final: 0.7360 (t) REVERT: F 4 LEU cc_start: 0.8081 (mt) cc_final: 0.7814 (mm) REVERT: F 15 LEU cc_start: 0.8081 (tp) cc_final: 0.7727 (mm) REVERT: F 93 GLU cc_start: 0.8582 (pm20) cc_final: 0.7679 (pm20) REVERT: G 757 MET cc_start: 0.8394 (mmt) cc_final: 0.8179 (mmt) REVERT: H 39 GLN cc_start: 0.8464 (tt0) cc_final: 0.7915 (tt0) REVERT: H 59 TYR cc_start: 0.8114 (m-10) cc_final: 0.7761 (m-10) REVERT: H 81 GLU cc_start: 0.8540 (tt0) cc_final: 0.8275 (mp0) REVERT: H 85 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8337 (mp0) REVERT: p 100 LEU cc_start: 0.7664 (mm) cc_final: 0.7286 (mm) REVERT: p 147 PHE cc_start: 0.8388 (m-80) cc_final: 0.7576 (m-80) REVERT: p 563 MET cc_start: 0.3757 (ptp) cc_final: 0.2489 (tpp) REVERT: p 696 MET cc_start: 0.4240 (ppp) cc_final: 0.3203 (ppp) REVERT: q 148 MET cc_start: 0.8426 (ttt) cc_final: 0.7819 (ttt) REVERT: q 278 MET cc_start: 0.8710 (mpp) cc_final: 0.8219 (mmm) REVERT: q 428 ILE cc_start: 0.7850 (tt) cc_final: 0.7630 (tt) REVERT: q 468 ASN cc_start: 0.4096 (m-40) cc_final: 0.3130 (m-40) REVERT: q 637 ASN cc_start: 0.8586 (t0) cc_final: 0.8180 (t0) REVERT: q 728 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7943 (tptt) REVERT: r 204 PHE cc_start: 0.8153 (t80) cc_final: 0.7906 (t80) REVERT: r 346 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: r 388 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5849 (mt) REVERT: r 592 ASN cc_start: 0.7622 (m-40) cc_final: 0.7202 (p0) REVERT: r 614 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: r 663 TYR cc_start: 0.8784 (t80) cc_final: 0.8514 (t80) outliers start: 72 outliers final: 58 residues processed: 359 average time/residue: 0.1999 time to fit residues: 122.4226 Evaluate side-chains 357 residues out of total 3654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 766 HIS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1181 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 806 CYS Chi-restraints excluded: chain G residue 1103 VAL Chi-restraints excluded: chain G residue 1117 CYS Chi-restraints excluded: chain G residue 1182 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain p residue 104 ASN Chi-restraints excluded: chain p residue 293 TYR Chi-restraints excluded: chain p residue 313 PHE Chi-restraints excluded: chain p residue 727 CYS Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 183 PHE Chi-restraints excluded: chain q residue 284 LEU Chi-restraints excluded: chain q residue 293 TYR Chi-restraints excluded: chain q residue 313 PHE Chi-restraints excluded: chain q residue 724 VAL Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 170 VAL Chi-restraints excluded: chain r residue 333 ILE Chi-restraints excluded: chain r residue 346 GLN Chi-restraints excluded: chain r residue 350 SER Chi-restraints excluded: chain r residue 356 VAL Chi-restraints excluded: chain r residue 363 VAL Chi-restraints excluded: chain r residue 388 LEU Chi-restraints excluded: chain r residue 443 LEU Chi-restraints excluded: chain r residue 512 THR Chi-restraints excluded: chain r residue 540 TYR Chi-restraints excluded: chain r residue 612 SER Chi-restraints excluded: chain r residue 614 ARG Chi-restraints excluded: chain r residue 665 LYS Chi-restraints excluded: chain r residue 693 THR Chi-restraints excluded: chain r residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 352 optimal weight: 2.9990 chunk 410 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 272 optimal weight: 0.0470 chunk 382 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 367 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27DASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1132 ASN H 6 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 167 HIS ** r 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 688 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.094989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070290 restraints weight = 152953.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072426 restraints weight = 77646.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073795 restraints weight = 50519.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074676 restraints weight = 38514.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.075177 restraints weight = 32573.086| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34737 Z= 0.123 Angle : 0.725 13.382 47374 Z= 0.352 Chirality : 0.048 0.418 5406 Planarity : 0.004 0.064 6024 Dihedral : 7.480 98.999 5952 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.90 % Favored : 94.87 % Rotamer: Outliers : 1.70 % Allowed : 15.96 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4227 helix: 1.53 (0.20), residues: 686 sheet: 0.25 (0.15), residues: 1088 loop : -0.46 (0.13), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG p 629 TYR 0.030 0.001 TYR D 777 PHE 0.031 0.001 PHE r 313 TRP 0.058 0.002 TRP F 35 HIS 0.008 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00261 (34617) covalent geometry : angle 0.69408 (47073) SS BOND : bond 0.00420 ( 56) SS BOND : angle 1.43177 ( 112) hydrogen bonds : bond 0.04178 ( 1252) hydrogen bonds : angle 5.23550 ( 3228) Misc. bond : bond 0.01836 ( 1) link_BETA1-4 : bond 0.00668 ( 21) link_BETA1-4 : angle 2.92563 ( 63) link_NAG-ASN : bond 0.00637 ( 42) link_NAG-ASN : angle 3.37061 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.58 seconds wall clock time: 114 minutes 20.24 seconds (6860.24 seconds total)