Starting phenix.real_space_refine on Sat Feb 7 01:10:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nc3_49240/02_2026/9nc3_49240.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.053 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 165 5.16 5 C 18071 2.51 5 N 4835 2.21 5 O 5750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3559 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 1 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3559 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 1 Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 993 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3559 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 1 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 950 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "G" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1699 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "H" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1573 Classifications: {'peptide': 210} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Chain: "I" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1753 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 215} Chain: "J" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1668 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "K" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "P" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 796 Classifications: {'peptide': 107} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "Q" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.12, per 1000 atoms: 0.21 Number of scatterers: 28821 At special positions: 0 Unit cell: (120.156, 167.586, 194.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 5750 8.00 N 4835 7.00 C 18071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.14 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.18 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.12 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.06 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.09 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.08 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.14 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.08 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.05 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.07 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.08 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 208 " distance=2.13 Simple disulfide: pdb=" SG CYS I 230 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.15 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.10 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " " MAN b 5 " - " MAN b 6 " ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 8 " " MAN b 4 " - " MAN b 7 " " BMA f 3 " - " MAN f 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA U 3 " - " MAN U 6 " " BMA Y 3 " - " MAN Y 5 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 5 " " BMA h 3 " - " MAN h 4 " " BMA p 3 " - " MAN p 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " BETA1-6 " NAG k 1 " - " FUC k 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 356 " " NAG A 607 " - " ASN A 396 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 356 " " NAG C 607 " - " ASN C 392 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 289 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 356 " " NAG E 608 " - " ASN E 448 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 241 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 276 " " NAG W 1 " - " ASN A 289 " " NAG X 1 " - " ASN A 295 " " NAG Y 1 " - " ASN A 362 " " NAG Z 1 " - " ASN A 392 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 386 " " NAG c 1 " - " ASN B 625 " " NAG d 1 " - " ASN C 88 " " NAG e 1 " - " ASN C 241 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 289 " " NAG h 1 " - " ASN C 362 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 448 " " NAG k 1 " - " ASN D 625 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 241 " " NAG n 1 " - " ASN E 262 " " NAG o 1 " - " ASN E 362 " " NAG p 1 " - " ASN E 386 " " NAG q 1 " - " ASN F 625 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6506 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 54 sheets defined 19.0% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.174A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.812A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.776A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 538 No H-bonds generated for 'chain 'B' and resid 537 through 538' Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.632A pdb=" N ASN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 596 removed outlier: 3.605A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 655 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.254A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.276A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 526 Processing helix chain 'D' and resid 529 through 543 Processing helix chain 'D' and resid 564 through 597 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.190A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.750A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.764A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.949A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'F' and resid 529 through 542 removed outlier: 3.622A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 597 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.875A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 100E through 100I removed outlier: 3.543A pdb=" N PHE G 100I" --> pdb=" O SER G 100F" (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.521A pdb=" N GLU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.654A pdb=" N HIS H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 196 through 203 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 183 through 187 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100E through 100I removed outlier: 3.529A pdb=" N PHE K 100I" --> pdb=" O SER K 100F" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.934A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.576A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100E through 100I removed outlier: 3.572A pdb=" N PHE O 100I" --> pdb=" O SER O 100F" (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.619A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.284A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.643A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.563A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 4.333A pdb=" N ASN A 190 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.036A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.533A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.327A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.600A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.847A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.516A pdb=" N ASN C 301 " --> pdb=" O ILE C 322A" (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.286A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.593A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.969A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.162A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.489A pdb=" N ASN E 301 " --> pdb=" O ILE E 322A" (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE E 322A" --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 322A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100K through 103 Processing sheet with id=AC7, first strand: chain 'G' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 145 current: chain 'G' and resid 176 through 185 Processing sheet with id=AC8, first strand: chain 'G' and resid 151 through 154 removed outlier: 3.536A pdb=" N THR G 151 " --> pdb=" O ASN G 199 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 13 current: chain 'H' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 48 current: chain 'H' and resid 95A through 98 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AD2, first strand: chain 'H' and resid 114 through 118 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 130 through 139 current: chain 'H' and resid 173 through 181 Processing sheet with id=AD3, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.096A pdb=" N TRP H 148 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100J through 103 Processing sheet with id=AD6, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.558A pdb=" N GLY I 141 " --> pdb=" O LEU I 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 138 through 147 current: chain 'I' and resid 185 through 193 Processing sheet with id=AD7, first strand: chain 'I' and resid 153 through 157 removed outlier: 3.731A pdb=" N TYR I 206 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 7 removed outlier: 6.144A pdb=" N THR J 69 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N HIS J 27 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N SER J 67 " --> pdb=" O HIS J 27 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ILE J 28A" --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N SER J 65 " --> pdb=" O ILE J 28A" (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 13 current: chain 'J' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 53 through 54 current: chain 'J' and resid 97 through 98 Processing sheet with id=AE1, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.582A pdb=" N ASN J 138 " --> pdb=" O TYR J 173 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100K through 103 Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95A through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 56 through 59 current: chain 'M' and resid 100J through 103 Processing sheet with id=AE9, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 12 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 97 through 98 Processing sheet with id=AF2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 12 current: chain 'O' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 102 through 103 Processing sheet with id=AF4, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 95A through 98 No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AF6, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 59 current: chain 'Q' and resid 100J through 103 Processing sheet with id=AF8, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 12 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 97 through 98 790 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5378 1.32 - 1.45: 7935 1.45 - 1.58: 15911 1.58 - 1.70: 0 1.70 - 1.83: 227 Bond restraints: 29451 Sorted by residual: bond pdb=" CB TRP I 50 " pdb=" CG TRP I 50 " ideal model delta sigma weight residual 1.498 1.397 0.101 3.10e-02 1.04e+03 1.06e+01 bond pdb=" CB HIS I 212 " pdb=" CG HIS I 212 " ideal model delta sigma weight residual 1.497 1.454 0.043 1.40e-02 5.10e+03 9.49e+00 bond pdb=" CB HIS E 330 " pdb=" CG HIS E 330 " ideal model delta sigma weight residual 1.497 1.455 0.042 1.40e-02 5.10e+03 9.06e+00 bond pdb=" CD ARG N 32 " pdb=" NE ARG N 32 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.40e-02 5.10e+03 7.70e+00 bond pdb=" CD GLU A 91 " pdb=" OE1 GLU A 91 " ideal model delta sigma weight residual 1.249 1.196 0.053 1.90e-02 2.77e+03 7.66e+00 ... (remaining 29446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 34114 1.59 - 3.18: 4718 3.18 - 4.76: 824 4.76 - 6.35: 291 6.35 - 7.94: 60 Bond angle restraints: 40007 Sorted by residual: angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 125.72 -6.06 7.30e-01 1.88e+00 6.89e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.39 -5.73 7.20e-01 1.93e+00 6.34e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.01e+00 9.80e-01 6.13e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 127.50 -7.94 1.02e+00 9.61e-01 6.06e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.36 -7.80 1.01e+00 9.80e-01 5.96e+01 ... (remaining 40002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 18222 21.15 - 42.30: 337 42.30 - 63.45: 142 63.45 - 84.59: 103 84.59 - 105.74: 52 Dihedral angle restraints: 18856 sinusoidal: 8719 harmonic: 10137 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -138.75 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -137.55 51.55 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS G 140 " pdb=" SG CYS G 140 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 45.08 47.92 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 18853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4594 0.154 - 0.308: 138 0.308 - 0.462: 4 0.462 - 0.616: 1 0.616 - 0.770: 1 Chirality restraints: 4738 Sorted by residual: chirality pdb=" C1 MAN U 4 " pdb=" O3 BMA U 3 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.10e+02 chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.44e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.30e+02 ... (remaining 4735 not shown) Planarity restraints: 5023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 332 " 0.064 2.00e-02 2.50e+03 6.65e-02 5.54e+01 pdb=" CG ASN E 332 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 332 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN E 332 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 130 " 0.037 2.00e-02 2.50e+03 3.86e-02 1.87e+01 pdb=" CG ASN E 130 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN E 130 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 130 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 295 " -0.036 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN C 295 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 295 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 295 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG C 603 " -0.044 2.00e-02 2.50e+03 ... (remaining 5020 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9726 2.85 - 3.36: 25082 3.36 - 3.88: 48708 3.88 - 4.39: 55005 4.39 - 4.90: 92798 Nonbonded interactions: 231319 Sorted by model distance: nonbonded pdb=" O3 NAG p 1 " pdb=" O5 NAG p 2 " model vdw 2.340 3.040 nonbonded pdb=" O3 NAG p 2 " pdb=" O5 BMA p 3 " model vdw 2.353 3.040 nonbonded pdb=" OG SER J 65 " pdb=" OG1 THR J 72 " model vdw 2.357 3.040 nonbonded pdb=" O3 NAG d 1 " pdb=" O5 NAG d 2 " model vdw 2.367 3.040 nonbonded pdb=" O3 NAG q 2 " pdb=" O5 BMA q 3 " model vdw 2.382 3.040 ... (remaining 231314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'E' and resid 34 through 607) } ncs_group { reference = (chain 'B' and (resid 519 through 542 or resid 563 through 653)) selection = (chain 'D' and (resid 519 through 542 or resid 563 through 653)) selection = (chain 'F' and resid 519 through 653) } ncs_group { reference = (chain 'K' and resid 3 through 112) selection = (chain 'O' and resid 3 through 112) } ncs_group { reference = (chain 'L' and resid 3 through 106) selection = chain 'P' } ncs_group { reference = (chain 'M' and resid 2 through 112) selection = chain 'Q' } ncs_group { reference = (chain 'N' and resid 2 through 105) selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'l' selection = chain 'm' } ncs_group { reference = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) } ncs_group { reference = chain 'f' selection = chain 'h' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.860 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.012 0.150 29601 Z= 0.637 Angle : 1.328 18.249 40407 Z= 0.842 Chirality : 0.067 0.770 4738 Planarity : 0.005 0.035 4976 Dihedral : 13.232 105.742 12200 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 3.26 (0.14), residues: 3472 helix: 0.16 (0.20), residues: 444 sheet: 1.95 (0.14), residues: 1133 loop : 3.17 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 480 TYR 0.051 0.004 TYR L 36 PHE 0.020 0.004 PHE M 45 TRP 0.029 0.005 TRP C 112 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.01127 (29451) covalent geometry : angle 1.24558 (40007) SS BOND : bond 0.04733 ( 50) SS BOND : angle 2.61423 ( 100) hydrogen bonds : bond 0.20925 ( 790) hydrogen bonds : angle 8.11146 ( 2019) link_ALPHA1-2 : bond 0.04577 ( 2) link_ALPHA1-2 : angle 6.28462 ( 6) link_ALPHA1-3 : bond 0.04587 ( 7) link_ALPHA1-3 : angle 4.74147 ( 21) link_ALPHA1-6 : bond 0.03685 ( 6) link_ALPHA1-6 : angle 5.13670 ( 18) link_BETA1-4 : bond 0.04644 ( 37) link_BETA1-4 : angle 7.27666 ( 111) link_BETA1-6 : bond 0.03506 ( 1) link_BETA1-6 : angle 8.52261 ( 3) link_NAG-ASN : bond 0.06664 ( 47) link_NAG-ASN : angle 2.88972 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 TRP cc_start: 0.8850 (m100) cc_final: 0.8320 (m100) REVERT: C 373 MET cc_start: 0.7377 (mtm) cc_final: 0.7014 (mtm) REVERT: J 158 ASN cc_start: 0.8178 (m-40) cc_final: 0.7909 (t0) REVERT: M 35 HIS cc_start: 0.5247 (m170) cc_final: 0.4671 (m170) REVERT: O 10 GLU cc_start: 0.8123 (tt0) cc_final: 0.7894 (tm-30) REVERT: O 105 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7964 (ptp90) REVERT: P 49 TYR cc_start: 0.5694 (t80) cc_final: 0.4988 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1981 time to fit residues: 50.5850 Evaluate side-chains 88 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 624 ASN E 190 ASN ** Q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.072270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054567 restraints weight = 149113.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.055586 restraints weight = 99975.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055954 restraints weight = 67719.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.056388 restraints weight = 60502.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.056377 restraints weight = 55939.497| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29601 Z= 0.126 Angle : 0.622 9.211 40407 Z= 0.309 Chirality : 0.045 0.252 4738 Planarity : 0.004 0.034 4976 Dihedral : 9.820 79.736 5842 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.33 % Allowed : 2.42 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 2.79 (0.14), residues: 3472 helix: 1.48 (0.22), residues: 449 sheet: 1.65 (0.14), residues: 1234 loop : 2.40 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 18 TYR 0.028 0.001 TYR J 140 PHE 0.031 0.002 PHE L 62 TRP 0.025 0.001 TRP D 571 HIS 0.012 0.001 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00266 (29451) covalent geometry : angle 0.58556 (40007) SS BOND : bond 0.00538 ( 50) SS BOND : angle 0.93628 ( 100) hydrogen bonds : bond 0.05137 ( 790) hydrogen bonds : angle 6.15602 ( 2019) link_ALPHA1-2 : bond 0.00570 ( 2) link_ALPHA1-2 : angle 2.95030 ( 6) link_ALPHA1-3 : bond 0.00784 ( 7) link_ALPHA1-3 : angle 2.31762 ( 21) link_ALPHA1-6 : bond 0.00431 ( 6) link_ALPHA1-6 : angle 1.94769 ( 18) link_BETA1-4 : bond 0.00500 ( 37) link_BETA1-4 : angle 3.04894 ( 111) link_BETA1-6 : bond 0.01702 ( 1) link_BETA1-6 : angle 5.39636 ( 3) link_NAG-ASN : bond 0.00247 ( 47) link_NAG-ASN : angle 1.79553 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.5530 (mmt) cc_final: 0.4589 (mtt) REVERT: B 629 MET cc_start: 0.7324 (mmm) cc_final: 0.7023 (mmm) REVERT: C 35 TRP cc_start: 0.8281 (m100) cc_final: 0.7788 (m100) REVERT: C 104 MET cc_start: 0.7450 (ttt) cc_final: 0.6784 (tmm) REVERT: C 373 MET cc_start: 0.6782 (mtm) cc_final: 0.6128 (mtm) REVERT: E 373 MET cc_start: 0.6061 (mtt) cc_final: 0.5814 (mtt) REVERT: F 530 MET cc_start: 0.7701 (mtp) cc_final: 0.7412 (mtp) REVERT: O 10 GLU cc_start: 0.8446 (tt0) cc_final: 0.8216 (tm-30) REVERT: O 34 MET cc_start: 0.7729 (tpt) cc_final: 0.7379 (tpp) REVERT: O 105 ARG cc_start: 0.7870 (ptt180) cc_final: 0.7659 (ptt-90) REVERT: O 108 MET cc_start: 0.7404 (tpp) cc_final: 0.7195 (tpp) outliers start: 10 outliers final: 3 residues processed: 103 average time/residue: 0.1864 time to fit residues: 31.9431 Evaluate side-chains 79 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain P residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 332 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 164 HIS H 38 GLN H 108 GLN I 6 GLN I 31 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS K 3 GLN O 6 GLN ** Q 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.068191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049584 restraints weight = 149939.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050734 restraints weight = 98083.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050798 restraints weight = 69714.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.051067 restraints weight = 67197.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051092 restraints weight = 61042.006| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 29601 Z= 0.306 Angle : 0.757 9.002 40407 Z= 0.380 Chirality : 0.050 0.260 4738 Planarity : 0.005 0.046 4976 Dihedral : 8.458 74.802 5842 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.49 % Allowed : 2.88 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.73 (0.14), residues: 3472 helix: 1.00 (0.23), residues: 456 sheet: 1.06 (0.14), residues: 1213 loop : 1.49 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 480 TYR 0.034 0.003 TYR Q 100I PHE 0.037 0.003 PHE I 45 TRP 0.029 0.002 TRP I 50 HIS 0.019 0.002 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00719 (29451) covalent geometry : angle 0.72788 (40007) SS BOND : bond 0.00426 ( 50) SS BOND : angle 1.05542 ( 100) hydrogen bonds : bond 0.05395 ( 790) hydrogen bonds : angle 6.01276 ( 2019) link_ALPHA1-2 : bond 0.00436 ( 2) link_ALPHA1-2 : angle 2.23916 ( 6) link_ALPHA1-3 : bond 0.00712 ( 7) link_ALPHA1-3 : angle 2.22136 ( 21) link_ALPHA1-6 : bond 0.00292 ( 6) link_ALPHA1-6 : angle 1.97585 ( 18) link_BETA1-4 : bond 0.00449 ( 37) link_BETA1-4 : angle 2.84440 ( 111) link_BETA1-6 : bond 0.01641 ( 1) link_BETA1-6 : angle 4.67819 ( 3) link_NAG-ASN : bond 0.00458 ( 47) link_NAG-ASN : angle 2.15328 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.8786 (mtt) cc_final: 0.8553 (mtt) REVERT: B 629 MET cc_start: 0.7555 (mmm) cc_final: 0.7262 (mmm) REVERT: C 104 MET cc_start: 0.7678 (ttt) cc_final: 0.7307 (ttp) REVERT: C 373 MET cc_start: 0.7731 (mtm) cc_final: 0.6696 (mtm) REVERT: E 373 MET cc_start: 0.7077 (mtt) cc_final: 0.6705 (mtt) REVERT: I 48 MET cc_start: 0.8622 (mtp) cc_final: 0.8385 (mtp) REVERT: J 173 TYR cc_start: 0.5553 (OUTLIER) cc_final: 0.5308 (m-10) REVERT: O 108 MET cc_start: 0.7746 (tpp) cc_final: 0.7388 (tpp) REVERT: Q 100 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6671 (p90) outliers start: 15 outliers final: 3 residues processed: 86 average time/residue: 0.1850 time to fit residues: 26.8478 Evaluate side-chains 74 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain J residue 173 TYR Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 100 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 68 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 251 optimal weight: 40.0000 chunk 284 optimal weight: 10.0000 chunk 274 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 280 ASN D 658 GLN F 650 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.068315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.051064 restraints weight = 147692.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.051168 restraints weight = 104741.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051454 restraints weight = 79766.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.051664 restraints weight = 73989.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.051734 restraints weight = 67485.702| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29601 Z= 0.217 Angle : 0.617 8.950 40407 Z= 0.305 Chirality : 0.046 0.267 4738 Planarity : 0.004 0.045 4976 Dihedral : 7.385 69.719 5842 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.69 % Allowed : 3.08 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.35 (0.14), residues: 3472 helix: 1.21 (0.24), residues: 457 sheet: 0.83 (0.14), residues: 1238 loop : 1.06 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.030 0.002 TYR G 33 PHE 0.022 0.002 PHE G 100K TRP 0.020 0.002 TRP I 50 HIS 0.021 0.002 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00502 (29451) covalent geometry : angle 0.58971 (40007) SS BOND : bond 0.00327 ( 50) SS BOND : angle 0.85800 ( 100) hydrogen bonds : bond 0.04268 ( 790) hydrogen bonds : angle 5.65963 ( 2019) link_ALPHA1-2 : bond 0.00580 ( 2) link_ALPHA1-2 : angle 2.15329 ( 6) link_ALPHA1-3 : bond 0.00858 ( 7) link_ALPHA1-3 : angle 2.38031 ( 21) link_ALPHA1-6 : bond 0.00478 ( 6) link_ALPHA1-6 : angle 1.92952 ( 18) link_BETA1-4 : bond 0.00374 ( 37) link_BETA1-4 : angle 2.42560 ( 111) link_BETA1-6 : bond 0.00921 ( 1) link_BETA1-6 : angle 4.88057 ( 3) link_NAG-ASN : bond 0.00261 ( 47) link_NAG-ASN : angle 1.79267 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: B 629 MET cc_start: 0.7587 (mmm) cc_final: 0.7294 (mmm) REVERT: C 373 MET cc_start: 0.7629 (mtm) cc_final: 0.6774 (mtm) REVERT: E 100 MET cc_start: 0.6640 (mtp) cc_final: 0.6167 (mtm) REVERT: E 373 MET cc_start: 0.7177 (mtt) cc_final: 0.6922 (mtt) REVERT: I 48 MET cc_start: 0.8632 (mtp) cc_final: 0.8363 (mtp) REVERT: M 100 MET cc_start: 0.7405 (mmm) cc_final: 0.7155 (mmm) REVERT: Q 100 MET cc_start: 0.5884 (mmm) cc_final: 0.5408 (mmm) outliers start: 21 outliers final: 12 residues processed: 90 average time/residue: 0.1562 time to fit residues: 25.0371 Evaluate side-chains 84 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 35 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 169 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 221 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 314 optimal weight: 50.0000 chunk 224 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 229 ASN I 6 GLN I 35 HIS ** I 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.051012 restraints weight = 148552.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051317 restraints weight = 101524.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051567 restraints weight = 76452.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051801 restraints weight = 70877.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.051899 restraints weight = 64285.338| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29601 Z= 0.152 Angle : 0.558 10.639 40407 Z= 0.273 Chirality : 0.044 0.244 4738 Planarity : 0.004 0.046 4976 Dihedral : 6.898 66.344 5842 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.59 % Allowed : 3.76 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.34 (0.14), residues: 3472 helix: 1.43 (0.24), residues: 457 sheet: 0.82 (0.14), residues: 1230 loop : 1.00 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 105 TYR 0.022 0.001 TYR G 33 PHE 0.017 0.001 PHE I 45 TRP 0.019 0.001 TRP D 571 HIS 0.009 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00352 (29451) covalent geometry : angle 0.53285 (40007) SS BOND : bond 0.00254 ( 50) SS BOND : angle 0.83490 ( 100) hydrogen bonds : bond 0.03808 ( 790) hydrogen bonds : angle 5.43020 ( 2019) link_ALPHA1-2 : bond 0.00484 ( 2) link_ALPHA1-2 : angle 1.97724 ( 6) link_ALPHA1-3 : bond 0.00809 ( 7) link_ALPHA1-3 : angle 2.18726 ( 21) link_ALPHA1-6 : bond 0.00471 ( 6) link_ALPHA1-6 : angle 1.86512 ( 18) link_BETA1-4 : bond 0.00341 ( 37) link_BETA1-4 : angle 2.22294 ( 111) link_BETA1-6 : bond 0.01021 ( 1) link_BETA1-6 : angle 4.70522 ( 3) link_NAG-ASN : bond 0.00190 ( 47) link_NAG-ASN : angle 1.60416 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 629 MET cc_start: 0.7433 (mmm) cc_final: 0.7120 (mmm) REVERT: C 373 MET cc_start: 0.7528 (mtm) cc_final: 0.6654 (mtm) REVERT: E 100 MET cc_start: 0.6787 (mtp) cc_final: 0.6302 (mtm) REVERT: E 373 MET cc_start: 0.7220 (mtt) cc_final: 0.6966 (mtt) REVERT: Q 100 MET cc_start: 0.6053 (mmm) cc_final: 0.5587 (mmm) outliers start: 18 outliers final: 10 residues processed: 87 average time/residue: 0.1477 time to fit residues: 22.8324 Evaluate side-chains 81 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 48 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 257 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 236 optimal weight: 3.9990 chunk 336 optimal weight: 0.0170 chunk 152 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 327 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 374 HIS E 229 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.068518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.051345 restraints weight = 148671.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.051396 restraints weight = 105500.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051628 restraints weight = 81376.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051900 restraints weight = 73455.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.051998 restraints weight = 66816.151| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29601 Z= 0.127 Angle : 0.520 8.450 40407 Z= 0.255 Chirality : 0.043 0.257 4738 Planarity : 0.003 0.045 4976 Dihedral : 6.401 61.002 5842 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.79 % Allowed : 3.80 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.40 (0.14), residues: 3472 helix: 1.66 (0.24), residues: 459 sheet: 0.90 (0.15), residues: 1202 loop : 0.93 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 18 TYR 0.020 0.001 TYR G 33 PHE 0.015 0.001 PHE I 45 TRP 0.018 0.001 TRP D 571 HIS 0.013 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00290 (29451) covalent geometry : angle 0.49682 (40007) SS BOND : bond 0.00220 ( 50) SS BOND : angle 0.73322 ( 100) hydrogen bonds : bond 0.03439 ( 790) hydrogen bonds : angle 5.19214 ( 2019) link_ALPHA1-2 : bond 0.00538 ( 2) link_ALPHA1-2 : angle 1.88298 ( 6) link_ALPHA1-3 : bond 0.00767 ( 7) link_ALPHA1-3 : angle 2.18689 ( 21) link_ALPHA1-6 : bond 0.00529 ( 6) link_ALPHA1-6 : angle 1.78886 ( 18) link_BETA1-4 : bond 0.00344 ( 37) link_BETA1-4 : angle 2.05210 ( 111) link_BETA1-6 : bond 0.01018 ( 1) link_BETA1-6 : angle 4.60567 ( 3) link_NAG-ASN : bond 0.00160 ( 47) link_NAG-ASN : angle 1.44051 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 629 MET cc_start: 0.7358 (mmm) cc_final: 0.7023 (mmm) REVERT: C 373 MET cc_start: 0.7482 (mtm) cc_final: 0.6570 (mtm) REVERT: E 100 MET cc_start: 0.6690 (mtp) cc_final: 0.6207 (mtm) REVERT: E 373 MET cc_start: 0.7316 (mtt) cc_final: 0.7077 (mtt) REVERT: J 48 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8209 (mm) REVERT: M 100 MET cc_start: 0.6944 (mmm) cc_final: 0.6710 (mmm) REVERT: O 72 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.7972 (t0) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.1517 time to fit residues: 25.2735 Evaluate side-chains 87 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 35 HIS Chi-restraints excluded: chain Q residue 48 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 171 optimal weight: 0.0060 chunk 17 optimal weight: 4.9990 chunk 139 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.068337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051119 restraints weight = 148730.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.051183 restraints weight = 106582.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.051531 restraints weight = 81156.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.051720 restraints weight = 74919.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051820 restraints weight = 68175.409| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29601 Z= 0.133 Angle : 0.523 8.136 40407 Z= 0.255 Chirality : 0.043 0.263 4738 Planarity : 0.003 0.046 4976 Dihedral : 6.237 59.095 5842 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.69 % Allowed : 4.22 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.37 (0.14), residues: 3472 helix: 1.78 (0.24), residues: 458 sheet: 0.87 (0.15), residues: 1200 loop : 0.89 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 480 TYR 0.018 0.001 TYR G 33 PHE 0.015 0.001 PHE I 45 TRP 0.017 0.001 TRP D 571 HIS 0.012 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00306 (29451) covalent geometry : angle 0.50095 (40007) SS BOND : bond 0.00226 ( 50) SS BOND : angle 0.75582 ( 100) hydrogen bonds : bond 0.03403 ( 790) hydrogen bonds : angle 5.12369 ( 2019) link_ALPHA1-2 : bond 0.00574 ( 2) link_ALPHA1-2 : angle 1.77642 ( 6) link_ALPHA1-3 : bond 0.00750 ( 7) link_ALPHA1-3 : angle 2.15714 ( 21) link_ALPHA1-6 : bond 0.00513 ( 6) link_ALPHA1-6 : angle 1.72718 ( 18) link_BETA1-4 : bond 0.00332 ( 37) link_BETA1-4 : angle 1.99566 ( 111) link_BETA1-6 : bond 0.00974 ( 1) link_BETA1-6 : angle 4.47887 ( 3) link_NAG-ASN : bond 0.00174 ( 47) link_NAG-ASN : angle 1.43910 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 629 MET cc_start: 0.7440 (mmm) cc_final: 0.7079 (mmm) REVERT: C 373 MET cc_start: 0.7491 (mtm) cc_final: 0.6574 (mtm) REVERT: D 530 MET cc_start: 0.8611 (mmm) cc_final: 0.7999 (mtp) REVERT: E 100 MET cc_start: 0.6793 (mtp) cc_final: 0.6299 (mtm) REVERT: E 373 MET cc_start: 0.7433 (mtt) cc_final: 0.7214 (mtt) REVERT: J 48 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8258 (mm) REVERT: O 72 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7987 (t0) REVERT: Q 100 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.7033 (p90) REVERT: Q 100 MET cc_start: 0.5965 (mmm) cc_final: 0.5731 (mmm) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.1624 time to fit residues: 25.4432 Evaluate side-chains 88 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 88 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 294 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 374 HIS C 374 HIS D 624 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN N 49 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.066657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049176 restraints weight = 150667.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049138 restraints weight = 106902.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.049371 restraints weight = 85241.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.049527 restraints weight = 77798.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.049842 restraints weight = 72260.732| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 29601 Z= 0.255 Angle : 0.643 8.370 40407 Z= 0.318 Chirality : 0.046 0.284 4738 Planarity : 0.004 0.044 4976 Dihedral : 6.724 59.068 5842 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.79 % Allowed : 4.29 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 0.81 (0.14), residues: 3472 helix: 1.11 (0.24), residues: 462 sheet: 0.55 (0.15), residues: 1161 loop : 0.54 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.022 0.002 TYR G 33 PHE 0.026 0.002 PHE I 45 TRP 0.015 0.002 TRP D 571 HIS 0.010 0.002 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00598 (29451) covalent geometry : angle 0.61959 (40007) SS BOND : bond 0.00382 ( 50) SS BOND : angle 1.00422 ( 100) hydrogen bonds : bond 0.04431 ( 790) hydrogen bonds : angle 5.51798 ( 2019) link_ALPHA1-2 : bond 0.00634 ( 2) link_ALPHA1-2 : angle 1.73925 ( 6) link_ALPHA1-3 : bond 0.00696 ( 7) link_ALPHA1-3 : angle 2.32708 ( 21) link_ALPHA1-6 : bond 0.00488 ( 6) link_ALPHA1-6 : angle 1.69740 ( 18) link_BETA1-4 : bond 0.00340 ( 37) link_BETA1-4 : angle 2.20427 ( 111) link_BETA1-6 : bond 0.00906 ( 1) link_BETA1-6 : angle 4.20482 ( 3) link_NAG-ASN : bond 0.00367 ( 47) link_NAG-ASN : angle 1.84765 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: B 629 MET cc_start: 0.7585 (mmm) cc_final: 0.7294 (mmm) REVERT: C 373 MET cc_start: 0.7521 (mtm) cc_final: 0.6577 (mtm) REVERT: D 530 MET cc_start: 0.8831 (mmm) cc_final: 0.8485 (mtp) REVERT: J 48 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8698 (mm) REVERT: O 72 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.7934 (t0) REVERT: Q 100 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7164 (p90) outliers start: 24 outliers final: 13 residues processed: 91 average time/residue: 0.1526 time to fit residues: 24.9536 Evaluate side-chains 87 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 234 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 266 optimal weight: 20.0000 chunk 281 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 249 HIS A 374 HIS C 374 HIS H 93 ASN R 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.068343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.050134 restraints weight = 151091.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050541 restraints weight = 105887.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.050661 restraints weight = 82147.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.050892 restraints weight = 81795.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.050931 restraints weight = 69771.250| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29601 Z= 0.137 Angle : 0.540 11.959 40407 Z= 0.263 Chirality : 0.043 0.271 4738 Planarity : 0.003 0.044 4976 Dihedral : 6.296 59.878 5842 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.69 % Allowed : 4.38 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.02 (0.14), residues: 3472 helix: 1.53 (0.24), residues: 464 sheet: 0.60 (0.15), residues: 1181 loop : 0.66 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 490 TYR 0.019 0.001 TYR G 33 PHE 0.015 0.001 PHE K 29 TRP 0.019 0.001 TRP D 571 HIS 0.010 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00315 (29451) covalent geometry : angle 0.51800 (40007) SS BOND : bond 0.00230 ( 50) SS BOND : angle 0.84374 ( 100) hydrogen bonds : bond 0.03505 ( 790) hydrogen bonds : angle 5.22011 ( 2019) link_ALPHA1-2 : bond 0.00528 ( 2) link_ALPHA1-2 : angle 1.86464 ( 6) link_ALPHA1-3 : bond 0.00718 ( 7) link_ALPHA1-3 : angle 2.16754 ( 21) link_ALPHA1-6 : bond 0.00571 ( 6) link_ALPHA1-6 : angle 1.64968 ( 18) link_BETA1-4 : bond 0.00330 ( 37) link_BETA1-4 : angle 1.93912 ( 111) link_BETA1-6 : bond 0.00940 ( 1) link_BETA1-6 : angle 4.50623 ( 3) link_NAG-ASN : bond 0.00165 ( 47) link_NAG-ASN : angle 1.48637 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: B 629 MET cc_start: 0.7381 (mmm) cc_final: 0.7045 (mmm) REVERT: C 373 MET cc_start: 0.7577 (mtm) cc_final: 0.6589 (mtm) REVERT: D 530 MET cc_start: 0.8667 (mmm) cc_final: 0.8009 (mtp) REVERT: E 373 MET cc_start: 0.7391 (mtt) cc_final: 0.7036 (mtt) REVERT: J 48 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8264 (mm) REVERT: O 72 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7868 (t0) REVERT: Q 100 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7097 (p90) outliers start: 21 outliers final: 17 residues processed: 89 average time/residue: 0.1639 time to fit residues: 25.5156 Evaluate side-chains 91 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 35 HIS Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 314 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 218 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.067394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.049253 restraints weight = 150565.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.049646 restraints weight = 104907.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.049890 restraints weight = 77118.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.050088 restraints weight = 75006.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050121 restraints weight = 67791.492| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29601 Z= 0.145 Angle : 0.542 12.856 40407 Z= 0.264 Chirality : 0.043 0.278 4738 Planarity : 0.003 0.044 4976 Dihedral : 6.160 59.422 5842 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.69 % Allowed : 4.45 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 1.02 (0.14), residues: 3472 helix: 1.65 (0.24), residues: 458 sheet: 0.63 (0.15), residues: 1158 loop : 0.61 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 105 TYR 0.019 0.001 TYR N 91 PHE 0.015 0.001 PHE I 45 TRP 0.018 0.001 TRP D 571 HIS 0.024 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (29451) covalent geometry : angle 0.52047 (40007) SS BOND : bond 0.00245 ( 50) SS BOND : angle 0.82092 ( 100) hydrogen bonds : bond 0.03508 ( 790) hydrogen bonds : angle 5.19777 ( 2019) link_ALPHA1-2 : bond 0.00595 ( 2) link_ALPHA1-2 : angle 1.74884 ( 6) link_ALPHA1-3 : bond 0.00706 ( 7) link_ALPHA1-3 : angle 2.18266 ( 21) link_ALPHA1-6 : bond 0.00554 ( 6) link_ALPHA1-6 : angle 1.63828 ( 18) link_BETA1-4 : bond 0.00324 ( 37) link_BETA1-4 : angle 1.92774 ( 111) link_BETA1-6 : bond 0.00942 ( 1) link_BETA1-6 : angle 4.33138 ( 3) link_NAG-ASN : bond 0.00181 ( 47) link_NAG-ASN : angle 1.50003 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: B 629 MET cc_start: 0.7394 (mmm) cc_final: 0.7062 (mmm) REVERT: C 373 MET cc_start: 0.7560 (mtm) cc_final: 0.6642 (mtm) REVERT: C 475 MET cc_start: 0.8469 (tpp) cc_final: 0.7954 (tpp) REVERT: D 530 MET cc_start: 0.8706 (mmm) cc_final: 0.8047 (mtp) REVERT: E 373 MET cc_start: 0.7441 (mtt) cc_final: 0.7177 (mtt) REVERT: F 535 MET cc_start: 0.7470 (mtm) cc_final: 0.7241 (mpp) REVERT: J 48 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8539 (mm) REVERT: O 72 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7821 (t0) REVERT: O 108 MET cc_start: 0.8357 (tpp) cc_final: 0.7983 (tpp) REVERT: Q 100 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7097 (p90) outliers start: 21 outliers final: 16 residues processed: 90 average time/residue: 0.1626 time to fit residues: 26.0719 Evaluate side-chains 90 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain Q residue 35 HIS Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 336 optimal weight: 0.0000 chunk 165 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 374 HIS R 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.068005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.050760 restraints weight = 149548.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.050772 restraints weight = 105596.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051060 restraints weight = 82787.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.051264 restraints weight = 75583.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051325 restraints weight = 70032.797| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29601 Z= 0.149 Angle : 0.536 11.306 40407 Z= 0.262 Chirality : 0.043 0.288 4738 Planarity : 0.004 0.044 4976 Dihedral : 5.920 59.590 5842 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.59 % Cis-general : 0.09 % 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: 0.99 (0.14), residues: 3472 helix: 1.70 (0.24), residues: 458 sheet: 0.60 (0.15), residues: 1147 loop : 0.58 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 105 TYR 0.026 0.001 TYR N 91 PHE 0.016 0.001 PHE I 45 TRP 0.018 0.001 TRP D 571 HIS 0.010 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00348 (29451) covalent geometry : angle 0.51492 (40007) SS BOND : bond 0.00245 ( 50) SS BOND : angle 0.79720 ( 100) hydrogen bonds : bond 0.03481 ( 790) hydrogen bonds : angle 5.15657 ( 2019) link_ALPHA1-2 : bond 0.00606 ( 2) link_ALPHA1-2 : angle 1.70634 ( 6) link_ALPHA1-3 : bond 0.00687 ( 7) link_ALPHA1-3 : angle 2.12851 ( 21) link_ALPHA1-6 : bond 0.00605 ( 6) link_ALPHA1-6 : angle 1.57386 ( 18) link_BETA1-4 : bond 0.00325 ( 37) link_BETA1-4 : angle 1.87878 ( 111) link_BETA1-6 : bond 0.00916 ( 1) link_BETA1-6 : angle 4.22625 ( 3) link_NAG-ASN : bond 0.00180 ( 47) link_NAG-ASN : angle 1.49349 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.49 seconds wall clock time: 67 minutes 23.82 seconds (4043.82 seconds total)