Starting phenix.real_space_refine on Fri Sep 19 11:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516.map" model { file = "/net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cm3_7516/09_2025/6cm3_7516_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 216 atoms to isotropic. 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 129 5.16 5 C 16002 2.51 5 N 4248 2.21 5 O 5076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25455 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "K" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "O" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "U" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Z" 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: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "h" 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: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" C1 NAG Y 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG Y 1 " occ=0.69 residue: pdb=" C1 NAG Y 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG Y 2 " occ=0.65 residue: pdb=" C1 BMA Y 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA Y 3 " occ=0.92 residue: pdb=" C1 MAN Y 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN Y 4 " occ=0.85 residue: pdb=" C1 MAN Y 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN Y 5 " occ=0.79 residue: pdb=" C1 MAN Y 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN Y 6 " occ=0.66 residue: pdb=" C1 NAG c 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG c 1 " occ=0.69 residue: pdb=" C1 NAG c 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG c 2 " occ=0.65 residue: pdb=" C1 BMA c 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA c 3 " occ=0.92 residue: pdb=" C1 MAN c 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN c 4 " occ=0.85 residue: pdb=" C1 MAN c 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN c 5 " occ=0.79 residue: pdb=" C1 MAN c 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN c 6 " occ=0.66 ... (remaining 6 not shown) Time building chain proxies: 6.68, per 1000 atoms: 0.26 Number of scatterers: 25455 At special positions: 0 Unit cell: (157.2, 149.34, 138.86, 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 129 16.00 O 5076 8.00 N 4248 7.00 C 16002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=1.97 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS D 501 " distance=2.01 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " 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=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.05 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 99 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 99 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 99 " distance=2.02 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 89 " distance=2.04 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=3, symmetry=0 Links applied ALPHA1-2 " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Z 4 " - " MAN Z 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN c 8 " - " MAN c 9 " " MAN d 4 " - " MAN d 5 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN g 8 " - " MAN g 9 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " MAN c 7 " - " MAN c 10 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 10 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 8 " " BMA a 3 " - " MAN a 5 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA e 3 " - " MAN e 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 5 " BETA1-4 " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG D 621 " - " ASN D 295 " " NAG D 622 " - " ASN D 332 " " NAG D 623 " - " ASN D 339 " " NAG D 624 " - " ASN D 363 " " NAG D 627 " - " ASN D 392 " " NAG D 628 " - " ASN D 448 " " NAG E 621 " - " ASN E 295 " " NAG E 622 " - " ASN E 332 " " NAG E 623 " - " ASN E 339 " " NAG E 624 " - " ASN E 363 " " NAG E 627 " - " ASN E 392 " " NAG E 628 " - " ASN E 448 " " NAG F 621 " - " ASN F 295 " " NAG F 622 " - " ASN F 332 " " NAG F 623 " - " ASN F 339 " " NAG F 624 " - " ASN F 363 " " NAG F 627 " - " ASN F 392 " " NAG F 628 " - " ASN F 448 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN C 637 " " NAG Y 1 " - " ASN D 234 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 386 " " NAG c 1 " - " ASN E 234 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN F 234 " " NAG h 1 " - " ASN F 262 " " NAG i 1 " - " ASN F 276 " " NAG j 1 " - " ASN F 386 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5838 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 60 sheets defined 15.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 525 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.990A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 593 removed outlier: 3.985A pdb=" N VAL A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TRP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.991A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 593 removed outlier: 3.986A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 544 removed outlier: 3.991A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 593 removed outlier: 3.985A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'D' and resid 64 through 74 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'D' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 98' Processing helix chain 'E' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 74 Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 98' Processing helix chain 'F' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU G 61 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU H 61 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP H 63 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU I 61 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.715A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.716A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.715A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 56 Processing helix chain 'R' and resid 53 through 56 Processing helix chain 'T' and resid 53 through 56 Processing sheet with id=AA1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.712A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE D 201 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 120 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.031A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS D 296 " --> pdb=" O CYS D 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 294 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.031A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS D 296 " --> pdb=" O CYS D 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 294 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.713A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE E 201 " --> pdb=" O LYS E 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 120 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 294 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 294 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.712A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE F 201 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 120 " --> pdb=" O MET F 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE G 67 " --> pdb=" O CYS G 16 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP H 28 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE H 67 " --> pdb=" O CYS H 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP I 28 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE I 67 " --> pdb=" O CYS I 16 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.564A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.666A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU K 10 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 33 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR K 32 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE K 52 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU K 10 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AD1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.565A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.665A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU M 10 " --> pdb=" O LEU M 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER M 33 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR M 32 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU M 10 " --> pdb=" O LEU M 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AD7, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.564A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.665A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU O 10 " --> pdb=" O LEU O 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER O 33 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR O 32 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE O 52 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG O 50 " --> pdb=" O PHE O 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU O 10 " --> pdb=" O LEU O 123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 18 through 20 Processing sheet with id=AE4, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'P' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 112 through 113 Processing sheet with id=AE8, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR Q 98 " --> pdb=" O GLN Q 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE Q 87 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR Q 103 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'R' and resid 112 through 113 Processing sheet with id=AF6, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR S 98 " --> pdb=" O GLN S 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE S 87 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR S 103 " --> pdb=" O PHE S 87 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'T' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'T' and resid 112 through 113 Processing sheet with id=AG4, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.503A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR U 98 " --> pdb=" O GLN U 91 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.503A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE U 87 " --> pdb=" O THR U 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR U 103 " --> pdb=" O PHE U 87 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2349 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: 5.16 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7698 1.33 - 1.46: 6034 1.46 - 1.58: 12086 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 25986 Sorted by residual: bond pdb=" CB TRP E 45 " pdb=" CG TRP E 45 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 8.95e+00 bond pdb=" CB TRP F 45 " pdb=" CG TRP F 45 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.89e+00 bond pdb=" CB TRP D 45 " pdb=" CG TRP D 45 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.87e+00 bond pdb=" CB TRP C 631 " pdb=" CG TRP C 631 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.47e+00 bond pdb=" CB TRP B 631 " pdb=" CG TRP B 631 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.44e+00 ... (remaining 25981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 34406 2.99 - 5.98: 823 5.98 - 8.97: 98 8.97 - 11.96: 7 11.96 - 14.95: 6 Bond angle restraints: 35340 Sorted by residual: angle pdb=" C CYS F 54 " pdb=" N ALA F 55 " pdb=" CA ALA F 55 " ideal model delta sigma weight residual 121.70 134.83 -13.13 1.80e+00 3.09e-01 5.32e+01 angle pdb=" C CYS D 54 " pdb=" N ALA D 55 " pdb=" CA ALA D 55 " ideal model delta sigma weight residual 121.70 134.82 -13.12 1.80e+00 3.09e-01 5.31e+01 angle pdb=" C CYS E 54 " pdb=" N ALA E 55 " pdb=" CA ALA E 55 " ideal model delta sigma weight residual 121.70 134.81 -13.11 1.80e+00 3.09e-01 5.31e+01 angle pdb=" C SER F 463 " pdb=" N THR F 464 " pdb=" CA THR F 464 " ideal model delta sigma weight residual 121.70 130.13 -8.43 1.80e+00 3.09e-01 2.19e+01 angle pdb=" C SER D 463 " pdb=" N THR D 464 " pdb=" CA THR D 464 " ideal model delta sigma weight residual 121.70 130.09 -8.39 1.80e+00 3.09e-01 2.17e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 15939 22.09 - 44.17: 428 44.17 - 66.26: 52 66.26 - 88.35: 69 88.35 - 110.44: 36 Dihedral angle restraints: 16524 sinusoidal: 7443 harmonic: 9081 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.89 72.89 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.89 72.89 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.88 72.88 1 1.00e+01 1.00e-02 6.77e+01 ... (remaining 16521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3991 0.124 - 0.248: 262 0.248 - 0.371: 16 0.371 - 0.495: 6 0.495 - 0.619: 3 Chirality restraints: 4278 Sorted by residual: chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 234 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 4275 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 610 " 0.031 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP B 610 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 610 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 610 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 610 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 610 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 610 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 610 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 610 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 610 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 610 " 0.031 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 610 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 610 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 610 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 610 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 610 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 610 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 610 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 610 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 610 " -0.031 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 610 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 610 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 610 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 610 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 610 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 610 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 610 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 610 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 610 " 0.003 2.00e-02 2.50e+03 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 244 2.62 - 3.19: 20866 3.19 - 3.76: 37179 3.76 - 4.33: 52174 4.33 - 4.90: 87246 Nonbonded interactions: 197709 Sorted by model distance: nonbonded pdb=" OG SER L 22 " pdb=" OE2 GLU L 70 " model vdw 2.044 3.040 nonbonded pdb=" OG SER N 22 " pdb=" OE2 GLU N 70 " model vdw 2.045 3.040 nonbonded pdb=" OG SER J 22 " pdb=" OE2 GLU J 70 " model vdw 2.045 3.040 nonbonded pdb=" OD2 ASP A 632 " pdb=" NE1 TRP R 108 " model vdw 2.118 3.120 nonbonded pdb=" OD2 ASP B 632 " pdb=" NE1 TRP P 108 " model vdw 2.168 3.120 ... (remaining 197704 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'f' selection = chain 'j' } ncs_group { reference = chain 'Y' selection = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'i' } 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=0.65 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.690 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.010 0.093 26124 Z= 0.412 Angle : 1.109 14.946 35700 Z= 0.546 Chirality : 0.070 0.619 4278 Planarity : 0.007 0.068 4350 Dihedral : 12.581 110.435 10551 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.11 % Allowed : 1.71 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.10 (0.13), residues: 3099 helix: -3.15 (0.16), residues: 450 sheet: -2.01 (0.15), residues: 1110 loop : -3.13 (0.13), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 327 TYR 0.043 0.004 TYR N 98 PHE 0.041 0.005 PHE D 382 TRP 0.055 0.005 TRP B 610 HIS 0.009 0.002 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00955 (25986) covalent geometry : angle 1.08080 (35340) SS BOND : bond 0.01535 ( 45) SS BOND : angle 1.69117 ( 90) hydrogen bonds : bond 0.17314 ( 849) hydrogen bonds : angle 8.24418 ( 2349) Misc. bond : bond 0.00566 ( 3) link_ALPHA1-2 : bond 0.00689 ( 12) link_ALPHA1-2 : angle 1.38552 ( 36) link_ALPHA1-3 : bond 0.00756 ( 12) link_ALPHA1-3 : angle 1.02593 ( 36) link_ALPHA1-6 : bond 0.00917 ( 9) link_ALPHA1-6 : angle 1.99341 ( 27) link_BETA1-4 : bond 0.00975 ( 24) link_BETA1-4 : angle 3.01650 ( 72) link_NAG-ASN : bond 0.00772 ( 33) link_NAG-ASN : angle 3.93708 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 943 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7647 (m-40) cc_final: 0.7246 (m-40) REVERT: A 620 SER cc_start: 0.8287 (m) cc_final: 0.7696 (t) REVERT: A 624 ASP cc_start: 0.8150 (m-30) cc_final: 0.7923 (m-30) REVERT: B 543 ASN cc_start: 0.7616 (m-40) cc_final: 0.7216 (m110) REVERT: B 620 SER cc_start: 0.8373 (m) cc_final: 0.8151 (t) REVERT: B 624 ASP cc_start: 0.7773 (m-30) cc_final: 0.7508 (m-30) REVERT: B 643 TYR cc_start: 0.9161 (m-10) cc_final: 0.8952 (m-10) REVERT: C 528 SER cc_start: 0.9335 (p) cc_final: 0.9018 (m) REVERT: C 586 TYR cc_start: 0.8178 (t80) cc_final: 0.7752 (t80) REVERT: C 620 SER cc_start: 0.8343 (m) cc_final: 0.8038 (p) REVERT: C 624 ASP cc_start: 0.7552 (m-30) cc_final: 0.7274 (m-30) REVERT: D 83 GLU cc_start: 0.7664 (tt0) cc_final: 0.7396 (tt0) REVERT: D 104 MET cc_start: 0.8145 (ptm) cc_final: 0.7695 (ttt) REVERT: D 193 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6197 (tm) REVERT: D 217 TYR cc_start: 0.7997 (m-80) cc_final: 0.7520 (m-80) REVERT: D 358 ILE cc_start: 0.7662 (mm) cc_final: 0.7411 (mt) REVERT: D 435 TYR cc_start: 0.8709 (m-10) cc_final: 0.8208 (m-10) REVERT: D 475 MET cc_start: 0.8319 (mmp) cc_final: 0.8061 (mmp) REVERT: E 83 GLU cc_start: 0.7701 (tt0) cc_final: 0.7333 (tt0) REVERT: E 107 ASP cc_start: 0.7813 (m-30) cc_final: 0.7193 (m-30) REVERT: E 193 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6187 (tm) REVERT: E 217 TYR cc_start: 0.7936 (m-80) cc_final: 0.7528 (m-80) REVERT: E 457 ASP cc_start: 0.7570 (m-30) cc_final: 0.7313 (m-30) REVERT: F 193 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6270 (tm) REVERT: F 264 SER cc_start: 0.8920 (m) cc_final: 0.8465 (p) REVERT: F 358 ILE cc_start: 0.7395 (mm) cc_final: 0.7066 (mt) REVERT: F 475 MET cc_start: 0.8450 (mmp) cc_final: 0.8065 (mmm) REVERT: H 24 ILE cc_start: 0.8917 (pt) cc_final: 0.8669 (tp) REVERT: H 42 SER cc_start: 0.9234 (p) cc_final: 0.8946 (t) REVERT: H 64 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8531 (mm-40) REVERT: I 2 LYS cc_start: 0.7073 (mttt) cc_final: 0.6855 (mmtm) REVERT: I 24 ILE cc_start: 0.8904 (pt) cc_final: 0.8363 (pt) REVERT: I 32 ASN cc_start: 0.8519 (m-40) cc_final: 0.8235 (t0) REVERT: J 23 CYS cc_start: 0.4532 (t) cc_final: 0.3044 (t) REVERT: J 32 ASP cc_start: 0.8026 (m-30) cc_final: 0.7669 (m-30) REVERT: J 37 GLN cc_start: 0.6901 (tt0) cc_final: 0.6532 (tt0) REVERT: J 61 ARG cc_start: 0.5879 (ptt-90) cc_final: 0.5387 (ptt90) REVERT: J 81 GLU cc_start: 0.7198 (pt0) cc_final: 0.6940 (mp0) REVERT: J 82 ASP cc_start: 0.5993 (m-30) cc_final: 0.4971 (m-30) REVERT: J 87 TYR cc_start: 0.7557 (m-80) cc_final: 0.7267 (m-10) REVERT: K 36 TRP cc_start: 0.7872 (m100) cc_final: 0.6851 (m100) REVERT: K 86 LEU cc_start: 0.8354 (mt) cc_final: 0.7888 (mt) REVERT: K 111 ASN cc_start: 0.8782 (t0) cc_final: 0.8413 (t0) REVERT: L 54 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: M 86 LEU cc_start: 0.8166 (mt) cc_final: 0.7919 (mt) REVERT: M 115 LEU cc_start: 0.8833 (mt) cc_final: 0.8538 (mt) REVERT: N 53 THR cc_start: 0.8830 (t) cc_final: 0.8559 (p) REVERT: N 79 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6642 (mm110) REVERT: O 67 ARG cc_start: 0.6887 (ptm160) cc_final: 0.5978 (ttt180) REVERT: O 87 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.7927 (mmp-170) REVERT: O 110 ASP cc_start: 0.7905 (m-30) cc_final: 0.7703 (m-30) REVERT: O 111 ASN cc_start: 0.8247 (t0) cc_final: 0.7825 (t0) REVERT: P 13 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7673 (mmtt) REVERT: Q 5 THR cc_start: 0.8596 (m) cc_final: 0.8388 (p) REVERT: R 52 ILE cc_start: 0.8685 (pt) cc_final: 0.7992 (mt) REVERT: R 93 ASP cc_start: 0.7863 (m-30) cc_final: 0.7354 (m-30) REVERT: T 93 ASP cc_start: 0.7932 (m-30) cc_final: 0.7601 (m-30) outliers start: 3 outliers final: 0 residues processed: 946 average time/residue: 0.1942 time to fit residues: 274.3340 Evaluate side-chains 591 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 588 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain F residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 616 ASN B 577 GLN B 611 ASN B 616 ASN C 611 ASN C 616 ASN D 66 HIS D 103 GLN D 258 GLN D 279 ASN D 280 ASN D 293 GLN E 66 HIS E 85 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 279 ASN E 280 ASN F 66 HIS F 85 HIS F 279 ASN F 280 ASN F 293 GLN F 422 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 94 GLN H 32 ASN H 94 GLN I 39 ASN I 73 ASN J 38 GLN K 39 GLN K 63 HIS K 65 GLN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN L 89 GLN L 90 GLN ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS N 37 GLN N 79 GLN N 89 GLN O 65 GLN P 28 ASN R 62 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098695 restraints weight = 41290.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102053 restraints weight = 21761.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104254 restraints weight = 14634.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105654 restraints weight = 11371.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106474 restraints weight = 9695.072| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26124 Z= 0.147 Angle : 0.767 14.706 35700 Z= 0.383 Chirality : 0.048 0.339 4278 Planarity : 0.005 0.058 4350 Dihedral : 11.648 82.142 5178 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.43 % Allowed : 11.12 % Favored : 85.45 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.14), residues: 3099 helix: -0.95 (0.24), residues: 390 sheet: -1.43 (0.16), residues: 1017 loop : -2.50 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 59 TYR 0.027 0.002 TYR N 49 PHE 0.018 0.002 PHE O 114 TRP 0.030 0.002 TRP Q 36 HIS 0.007 0.001 HIS M 117 Details of bonding type rmsd covalent geometry : bond 0.00324 (25986) covalent geometry : angle 0.73890 (35340) SS BOND : bond 0.00341 ( 45) SS BOND : angle 1.55724 ( 90) hydrogen bonds : bond 0.04442 ( 849) hydrogen bonds : angle 6.16137 ( 2349) Misc. bond : bond 0.01034 ( 3) link_ALPHA1-2 : bond 0.00709 ( 12) link_ALPHA1-2 : angle 1.90011 ( 36) link_ALPHA1-3 : bond 0.00780 ( 12) link_ALPHA1-3 : angle 1.76962 ( 36) link_ALPHA1-6 : bond 0.00575 ( 9) link_ALPHA1-6 : angle 1.71034 ( 27) link_BETA1-4 : bond 0.00816 ( 24) link_BETA1-4 : angle 2.41574 ( 72) link_NAG-ASN : bond 0.00292 ( 33) link_NAG-ASN : angle 2.78337 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 720 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7636 (m-40) cc_final: 0.7256 (m110) REVERT: A 610 TRP cc_start: 0.6305 (OUTLIER) cc_final: 0.5861 (m100) REVERT: A 620 SER cc_start: 0.8242 (m) cc_final: 0.7548 (t) REVERT: A 624 ASP cc_start: 0.7889 (m-30) cc_final: 0.7597 (m-30) REVERT: B 543 ASN cc_start: 0.7284 (m-40) cc_final: 0.7079 (m-40) REVERT: B 608 VAL cc_start: 0.9040 (t) cc_final: 0.8748 (p) REVERT: B 620 SER cc_start: 0.8131 (m) cc_final: 0.7722 (p) REVERT: B 624 ASP cc_start: 0.7715 (m-30) cc_final: 0.7299 (m-30) REVERT: B 643 TYR cc_start: 0.9153 (m-10) cc_final: 0.8939 (m-10) REVERT: C 620 SER cc_start: 0.8150 (m) cc_final: 0.7911 (p) REVERT: C 624 ASP cc_start: 0.7581 (m-30) cc_final: 0.7266 (m-30) REVERT: D 229 LYS cc_start: 0.8567 (mttt) cc_final: 0.8330 (mttt) REVERT: D 358 ILE cc_start: 0.7405 (mm) cc_final: 0.7134 (mt) REVERT: D 430 ILE cc_start: 0.9199 (mm) cc_final: 0.8934 (mm) REVERT: D 457 ASP cc_start: 0.7957 (m-30) cc_final: 0.7746 (m-30) REVERT: E 82 GLN cc_start: 0.7946 (mt0) cc_final: 0.7692 (pt0) REVERT: E 107 ASP cc_start: 0.8003 (m-30) cc_final: 0.7093 (m-30) REVERT: E 217 TYR cc_start: 0.7847 (m-80) cc_final: 0.7606 (m-80) REVERT: E 475 MET cc_start: 0.8050 (mmt) cc_final: 0.7550 (mmt) REVERT: F 91 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7204 (mm-30) REVERT: F 264 SER cc_start: 0.8777 (m) cc_final: 0.8323 (p) REVERT: F 327 ARG cc_start: 0.7242 (mpt-90) cc_final: 0.6990 (mpt-90) REVERT: F 358 ILE cc_start: 0.7018 (mm) cc_final: 0.6692 (mt) REVERT: F 475 MET cc_start: 0.8568 (mmp) cc_final: 0.7836 (mmm) REVERT: F 477 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: G 40 GLN cc_start: 0.8595 (mt0) cc_final: 0.8120 (mt0) REVERT: G 60 SER cc_start: 0.9324 (p) cc_final: 0.9117 (p) REVERT: G 87 GLU cc_start: 0.7058 (mp0) cc_final: 0.6688 (pm20) REVERT: G 89 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: H 32 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (t0) REVERT: H 40 GLN cc_start: 0.8492 (mt0) cc_final: 0.7852 (mt0) REVERT: H 64 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8663 (mm-40) REVERT: H 80 ASP cc_start: 0.7820 (t0) cc_final: 0.7606 (m-30) REVERT: I 32 ASN cc_start: 0.8511 (m-40) cc_final: 0.8139 (t0) REVERT: I 40 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7753 (mt0) REVERT: I 89 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: I 91 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6004 (tm-30) REVERT: J 21 LEU cc_start: 0.6520 (tp) cc_final: 0.6220 (tp) REVERT: J 37 GLN cc_start: 0.6564 (tt0) cc_final: 0.6310 (tt0) REVERT: J 82 ASP cc_start: 0.5989 (m-30) cc_final: 0.4766 (m-30) REVERT: K 12 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8394 (mmmt) REVERT: K 13 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7545 (mmtm) REVERT: K 19 LYS cc_start: 0.8671 (tptt) cc_final: 0.8420 (tptp) REVERT: K 56 ASP cc_start: 0.8302 (t0) cc_final: 0.8078 (m-30) REVERT: K 86 LEU cc_start: 0.8352 (mt) cc_final: 0.7933 (mt) REVERT: K 101 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7615 (mm-30) REVERT: K 111 ASN cc_start: 0.8697 (t0) cc_final: 0.8106 (t0) REVERT: L 5 THR cc_start: 0.8119 (p) cc_final: 0.7783 (m) REVERT: L 24 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7137 (tpp-160) REVERT: L 54 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: M 86 LEU cc_start: 0.8178 (mt) cc_final: 0.7771 (mt) REVERT: M 103 GLU cc_start: 0.6538 (pm20) cc_final: 0.5529 (pm20) REVERT: M 110 ASP cc_start: 0.7970 (m-30) cc_final: 0.7311 (t0) REVERT: M 111 ASN cc_start: 0.7840 (t0) cc_final: 0.7590 (t0) REVERT: M 114 PHE cc_start: 0.8224 (p90) cc_final: 0.7982 (p90) REVERT: M 120 GLN cc_start: 0.6968 (mm110) cc_final: 0.6739 (mp10) REVERT: N 53 THR cc_start: 0.8830 (t) cc_final: 0.8590 (p) REVERT: N 54 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7939 (mtm-85) REVERT: N 61 ARG cc_start: 0.5888 (ptt90) cc_final: 0.5369 (ptt90) REVERT: N 86 TYR cc_start: 0.6941 (m-10) cc_final: 0.6484 (m-10) REVERT: N 90 GLN cc_start: 0.8416 (pp30) cc_final: 0.8144 (pp30) REVERT: O 3 GLN cc_start: 0.6963 (mp10) cc_final: 0.6675 (mp10) REVERT: O 86 LEU cc_start: 0.8157 (mt) cc_final: 0.7774 (mt) REVERT: O 101 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7502 (mm-30) REVERT: O 110 ASP cc_start: 0.8031 (m-30) cc_final: 0.7291 (t0) REVERT: O 111 ASN cc_start: 0.8329 (t0) cc_final: 0.8052 (t0) REVERT: P 13 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7545 (mmmt) REVERT: R 89 LEU cc_start: 0.8339 (tp) cc_final: 0.8092 (tp) REVERT: T 89 LEU cc_start: 0.8561 (mm) cc_final: 0.8240 (mm) REVERT: U 6 GLN cc_start: 0.8226 (tt0) cc_final: 0.7988 (tt0) REVERT: U 40 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7815 (mmm-85) outliers start: 90 outliers final: 43 residues processed: 762 average time/residue: 0.1844 time to fit residues: 217.8894 Evaluate side-chains 646 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 598 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 610 TRP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 206 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 283 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 251 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN C 616 ASN E 103 GLN F 293 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 32 ASN H 94 GLN I 73 ASN I 94 GLN J 102 GLN K 63 HIS ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096548 restraints weight = 41811.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100124 restraints weight = 22815.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101914 restraints weight = 14214.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102167 restraints weight = 11632.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102374 restraints weight = 11009.965| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26124 Z= 0.197 Angle : 0.775 17.537 35700 Z= 0.380 Chirality : 0.049 0.507 4278 Planarity : 0.004 0.035 4350 Dihedral : 10.630 80.441 5178 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.27 % Allowed : 12.80 % Favored : 82.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.15), residues: 3099 helix: -0.34 (0.26), residues: 408 sheet: -1.20 (0.17), residues: 993 loop : -2.26 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 444 TYR 0.027 0.002 TYR J 49 PHE 0.017 0.002 PHE L 71 TRP 0.023 0.002 TRP B 610 HIS 0.005 0.001 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00457 (25986) covalent geometry : angle 0.74734 (35340) SS BOND : bond 0.00634 ( 45) SS BOND : angle 1.68327 ( 90) hydrogen bonds : bond 0.04185 ( 849) hydrogen bonds : angle 5.73873 ( 2349) Misc. bond : bond 0.00320 ( 3) link_ALPHA1-2 : bond 0.00308 ( 12) link_ALPHA1-2 : angle 1.86835 ( 36) link_ALPHA1-3 : bond 0.00797 ( 12) link_ALPHA1-3 : angle 1.75903 ( 36) link_ALPHA1-6 : bond 0.00545 ( 9) link_ALPHA1-6 : angle 1.67902 ( 27) link_BETA1-4 : bond 0.00869 ( 24) link_BETA1-4 : angle 2.41131 ( 72) link_NAG-ASN : bond 0.00377 ( 33) link_NAG-ASN : angle 2.71198 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 647 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7590 (m-40) cc_final: 0.7227 (m110) REVERT: A 620 SER cc_start: 0.8239 (m) cc_final: 0.7571 (t) REVERT: A 624 ASP cc_start: 0.7938 (m-30) cc_final: 0.7476 (m-30) REVERT: B 591 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8344 (tp40) REVERT: B 620 SER cc_start: 0.8087 (m) cc_final: 0.7715 (p) REVERT: B 624 ASP cc_start: 0.7703 (m-30) cc_final: 0.7309 (m-30) REVERT: C 585 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7936 (tpp-160) REVERT: C 620 SER cc_start: 0.8162 (m) cc_final: 0.7877 (p) REVERT: C 624 ASP cc_start: 0.7606 (m-30) cc_final: 0.7259 (m-30) REVERT: D 358 ILE cc_start: 0.7498 (mm) cc_final: 0.7240 (mt) REVERT: D 430 ILE cc_start: 0.9202 (mm) cc_final: 0.8932 (mm) REVERT: E 82 GLN cc_start: 0.8039 (mt0) cc_final: 0.7811 (pt0) REVERT: E 107 ASP cc_start: 0.8085 (m-30) cc_final: 0.6984 (m-30) REVERT: E 217 TYR cc_start: 0.7937 (m-80) cc_final: 0.7637 (m-80) REVERT: E 346 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8434 (p) REVERT: F 78 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7956 (t70) REVERT: F 358 ILE cc_start: 0.7076 (mm) cc_final: 0.6781 (mt) REVERT: F 475 MET cc_start: 0.8650 (mmp) cc_final: 0.8371 (tpp) REVERT: F 477 ASP cc_start: 0.8738 (m-30) cc_final: 0.8536 (m-30) REVERT: G 32 ASN cc_start: 0.8336 (t160) cc_final: 0.8072 (t0) REVERT: G 40 GLN cc_start: 0.8541 (mt0) cc_final: 0.8012 (mt0) REVERT: G 60 SER cc_start: 0.9408 (p) cc_final: 0.9170 (p) REVERT: H 40 GLN cc_start: 0.8624 (mt0) cc_final: 0.7955 (mt0) REVERT: H 64 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8649 (mm-40) REVERT: H 80 ASP cc_start: 0.7951 (t0) cc_final: 0.7616 (m-30) REVERT: I 32 ASN cc_start: 0.8575 (m-40) cc_final: 0.8188 (t0) REVERT: I 91 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6218 (tm-30) REVERT: J 5 THR cc_start: 0.8170 (p) cc_final: 0.7962 (m) REVERT: J 21 LEU cc_start: 0.6652 (tp) cc_final: 0.6300 (tp) REVERT: J 24 ARG cc_start: 0.8418 (tpm170) cc_final: 0.7684 (tpm170) REVERT: J 32 ASP cc_start: 0.8147 (m-30) cc_final: 0.7892 (m-30) REVERT: J 37 GLN cc_start: 0.6635 (tt0) cc_final: 0.6303 (tt0) REVERT: K 12 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8340 (mmmt) REVERT: K 13 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7533 (mmtm) REVERT: K 19 LYS cc_start: 0.8670 (tptt) cc_final: 0.8394 (tptp) REVERT: K 21 SER cc_start: 0.7466 (OUTLIER) cc_final: 0.7235 (t) REVERT: K 56 ASP cc_start: 0.8315 (t0) cc_final: 0.8100 (m-30) REVERT: K 86 LEU cc_start: 0.8378 (mt) cc_final: 0.7865 (mt) REVERT: K 101 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7629 (mm-30) REVERT: K 111 ASN cc_start: 0.8734 (t0) cc_final: 0.8229 (t0) REVERT: L 54 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8098 (mtm-85) REVERT: L 70 GLU cc_start: 0.6289 (tp30) cc_final: 0.6071 (tp30) REVERT: M 3 GLN cc_start: 0.7092 (mp10) cc_final: 0.6805 (mp10) REVERT: M 19 LYS cc_start: 0.8350 (tppt) cc_final: 0.8080 (tptp) REVERT: M 86 LEU cc_start: 0.7869 (mt) cc_final: 0.7651 (mt) REVERT: M 101 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7491 (mm-30) REVERT: M 103 GLU cc_start: 0.6692 (pm20) cc_final: 0.6317 (pm20) REVERT: M 110 ASP cc_start: 0.7950 (m-30) cc_final: 0.7190 (t0) REVERT: M 111 ASN cc_start: 0.7846 (t0) cc_final: 0.7562 (t0) REVERT: M 114 PHE cc_start: 0.8234 (p90) cc_final: 0.8008 (p90) REVERT: N 53 THR cc_start: 0.8818 (t) cc_final: 0.8577 (p) REVERT: N 61 ARG cc_start: 0.5807 (ptt90) cc_final: 0.5329 (ptt90) REVERT: N 90 GLN cc_start: 0.8344 (pp30) cc_final: 0.8059 (pp30) REVERT: O 3 GLN cc_start: 0.6883 (mp10) cc_final: 0.6609 (mp10) REVERT: O 19 LYS cc_start: 0.8875 (tptt) cc_final: 0.8502 (tptp) REVERT: O 21 SER cc_start: 0.7575 (OUTLIER) cc_final: 0.7086 (t) REVERT: O 73 ASP cc_start: 0.7946 (t70) cc_final: 0.7723 (t70) REVERT: O 86 LEU cc_start: 0.8109 (mt) cc_final: 0.7075 (mt) REVERT: O 87 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8070 (mmp-170) REVERT: O 101 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7387 (mm-30) REVERT: O 110 ASP cc_start: 0.8167 (m-30) cc_final: 0.7594 (t0) REVERT: O 111 ASN cc_start: 0.8339 (t0) cc_final: 0.7818 (t0) REVERT: P 13 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7570 (mmtt) REVERT: Q 3 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7549 (mm-40) REVERT: R 89 LEU cc_start: 0.8441 (tp) cc_final: 0.8174 (tp) REVERT: S 78 ASN cc_start: 0.7985 (t0) cc_final: 0.7692 (t0) REVERT: S 80 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8549 (mm110) REVERT: S 83 ASP cc_start: 0.8063 (m-30) cc_final: 0.7451 (m-30) REVERT: T 89 LEU cc_start: 0.8571 (mm) cc_final: 0.8269 (mm) REVERT: U 6 GLN cc_start: 0.8271 (tt0) cc_final: 0.7991 (tt0) outliers start: 112 outliers final: 67 residues processed: 703 average time/residue: 0.1854 time to fit residues: 202.2181 Evaluate side-chains 678 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 606 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 61 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 82 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 148 optimal weight: 0.0570 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN D 103 GLN D 216 HIS G 94 GLN H 94 GLN I 73 ASN I 94 GLN K 63 HIS K 117 HIS K 120 GLN M 65 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098035 restraints weight = 41349.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101422 restraints weight = 22020.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103617 restraints weight = 14842.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105003 restraints weight = 11567.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105839 restraints weight = 9895.937| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26124 Z= 0.127 Angle : 0.717 20.064 35700 Z= 0.353 Chirality : 0.047 0.371 4278 Planarity : 0.004 0.040 4350 Dihedral : 9.520 73.855 5178 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.04 % Allowed : 13.75 % Favored : 82.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.15), residues: 3099 helix: 0.05 (0.27), residues: 414 sheet: -0.88 (0.18), residues: 969 loop : -2.21 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 84 TYR 0.030 0.002 TYR J 49 PHE 0.020 0.002 PHE K 114 TRP 0.038 0.001 TRP K 36 HIS 0.015 0.001 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00278 (25986) covalent geometry : angle 0.69085 (35340) SS BOND : bond 0.00438 ( 45) SS BOND : angle 1.73229 ( 90) hydrogen bonds : bond 0.03630 ( 849) hydrogen bonds : angle 5.41671 ( 2349) Misc. bond : bond 0.00706 ( 3) link_ALPHA1-2 : bond 0.00313 ( 12) link_ALPHA1-2 : angle 1.94262 ( 36) link_ALPHA1-3 : bond 0.01097 ( 12) link_ALPHA1-3 : angle 1.59618 ( 36) link_ALPHA1-6 : bond 0.00742 ( 9) link_ALPHA1-6 : angle 1.71035 ( 27) link_BETA1-4 : bond 0.00799 ( 24) link_BETA1-4 : angle 2.16904 ( 72) link_NAG-ASN : bond 0.00297 ( 33) link_NAG-ASN : angle 2.37894 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 684 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7523 (m-40) cc_final: 0.7198 (m110) REVERT: A 620 SER cc_start: 0.8276 (m) cc_final: 0.7655 (t) REVERT: A 624 ASP cc_start: 0.7757 (m-30) cc_final: 0.7248 (m-30) REVERT: B 528 SER cc_start: 0.9311 (p) cc_final: 0.9053 (m) REVERT: B 620 SER cc_start: 0.7958 (m) cc_final: 0.7697 (p) REVERT: B 624 ASP cc_start: 0.7657 (m-30) cc_final: 0.7280 (m-30) REVERT: C 585 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7966 (tpp-160) REVERT: C 624 ASP cc_start: 0.7549 (m-30) cc_final: 0.7201 (m-30) REVERT: D 230 ASP cc_start: 0.7795 (t0) cc_final: 0.7570 (t0) REVERT: D 358 ILE cc_start: 0.7377 (mm) cc_final: 0.7121 (mt) REVERT: D 430 ILE cc_start: 0.9143 (mm) cc_final: 0.8862 (mm) REVERT: E 107 ASP cc_start: 0.8105 (m-30) cc_final: 0.7041 (m-30) REVERT: E 346 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8390 (p) REVERT: F 64 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7082 (tm-30) REVERT: F 78 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7736 (t70) REVERT: F 210 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: F 492 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: G 32 ASN cc_start: 0.8320 (t160) cc_final: 0.7948 (t0) REVERT: G 40 GLN cc_start: 0.8459 (mt0) cc_final: 0.7853 (mt0) REVERT: G 60 SER cc_start: 0.9395 (p) cc_final: 0.9143 (p) REVERT: H 32 ASN cc_start: 0.8390 (t0) cc_final: 0.8162 (t0) REVERT: H 40 GLN cc_start: 0.8433 (mt0) cc_final: 0.8026 (mt0) REVERT: H 64 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8560 (mm-40) REVERT: I 40 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7972 (mt0) REVERT: J 32 ASP cc_start: 0.7919 (m-30) cc_final: 0.7702 (m-30) REVERT: J 90 GLN cc_start: 0.8535 (pp30) cc_final: 0.8243 (pp30) REVERT: K 12 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8131 (mmmt) REVERT: K 13 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7597 (mmtm) REVERT: K 19 LYS cc_start: 0.8698 (tptt) cc_final: 0.8472 (tptp) REVERT: K 86 LEU cc_start: 0.8358 (mt) cc_final: 0.7792 (mt) REVERT: K 101 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7501 (mm-30) REVERT: K 111 ASN cc_start: 0.8749 (t0) cc_final: 0.8211 (t0) REVERT: L 71 PHE cc_start: 0.7869 (m-80) cc_final: 0.7595 (m-80) REVERT: L 90 GLN cc_start: 0.8155 (pp30) cc_final: 0.7689 (pp30) REVERT: M 3 GLN cc_start: 0.7123 (mp10) cc_final: 0.6919 (mp10) REVERT: M 19 LYS cc_start: 0.8388 (tppt) cc_final: 0.7821 (tptp) REVERT: M 101 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7563 (mm-30) REVERT: M 106 GLU cc_start: 0.8952 (pm20) cc_final: 0.8000 (pp20) REVERT: M 110 ASP cc_start: 0.7859 (m-30) cc_final: 0.7137 (t0) REVERT: M 114 PHE cc_start: 0.8262 (p90) cc_final: 0.8025 (p90) REVERT: N 23 CYS cc_start: 0.3978 (t) cc_final: 0.3719 (t) REVERT: N 53 THR cc_start: 0.8758 (t) cc_final: 0.8450 (p) REVERT: N 61 ARG cc_start: 0.5674 (ptt90) cc_final: 0.5273 (ptt90) REVERT: N 87 TYR cc_start: 0.7539 (m-80) cc_final: 0.7260 (m-80) REVERT: N 90 GLN cc_start: 0.8375 (pp30) cc_final: 0.8165 (pp30) REVERT: O 3 GLN cc_start: 0.6791 (mp10) cc_final: 0.6559 (mp10) REVERT: O 19 LYS cc_start: 0.8922 (tptt) cc_final: 0.8246 (tptt) REVERT: O 67 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: O 85 ASN cc_start: 0.7585 (t0) cc_final: 0.7120 (t0) REVERT: O 86 LEU cc_start: 0.7988 (mt) cc_final: 0.6892 (mt) REVERT: O 87 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8020 (mmp-170) REVERT: O 101 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7410 (mm-30) REVERT: O 110 ASP cc_start: 0.8150 (m-30) cc_final: 0.7608 (t0) REVERT: O 111 ASN cc_start: 0.8518 (t0) cc_final: 0.7964 (t0) REVERT: P 13 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7610 (mmtt) REVERT: P 101 THR cc_start: 0.8946 (p) cc_final: 0.8369 (p) REVERT: P 121 SER cc_start: 0.8821 (t) cc_final: 0.8546 (p) REVERT: R 89 LEU cc_start: 0.8393 (tp) cc_final: 0.8158 (tp) REVERT: S 83 ASP cc_start: 0.7879 (m-30) cc_final: 0.7425 (m-30) REVERT: S 101 GLN cc_start: 0.7797 (mt0) cc_final: 0.7388 (mm-40) REVERT: T 89 LEU cc_start: 0.8544 (mm) cc_final: 0.8282 (mm) REVERT: U 6 GLN cc_start: 0.8033 (tt0) cc_final: 0.7612 (tt0) outliers start: 106 outliers final: 58 residues processed: 741 average time/residue: 0.1789 time to fit residues: 206.9554 Evaluate side-chains 677 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 614 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 262 optimal weight: 0.0870 chunk 204 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 293 GLN G 32 ASN H 94 GLN I 73 ASN I 94 GLN K 63 HIS K 120 GLN M 111 ASN N 37 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 HIS Q 80 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096824 restraints weight = 41542.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100268 restraints weight = 22772.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102140 restraints weight = 14664.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102389 restraints weight = 11840.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102594 restraints weight = 11144.946| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26124 Z= 0.167 Angle : 0.753 21.543 35700 Z= 0.368 Chirality : 0.049 0.527 4278 Planarity : 0.004 0.037 4350 Dihedral : 8.923 72.653 5178 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.11 % Allowed : 15.05 % Favored : 80.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.15), residues: 3099 helix: 0.23 (0.27), residues: 414 sheet: -0.88 (0.17), residues: 987 loop : -2.07 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 64 TYR 0.032 0.002 TYR J 49 PHE 0.016 0.002 PHE J 71 TRP 0.051 0.001 TRP K 36 HIS 0.012 0.001 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00383 (25986) covalent geometry : angle 0.72128 (35340) SS BOND : bond 0.00553 ( 45) SS BOND : angle 2.12687 ( 90) hydrogen bonds : bond 0.03699 ( 849) hydrogen bonds : angle 5.29906 ( 2349) Misc. bond : bond 0.00817 ( 3) link_ALPHA1-2 : bond 0.00718 ( 12) link_ALPHA1-2 : angle 1.98072 ( 36) link_ALPHA1-3 : bond 0.00889 ( 12) link_ALPHA1-3 : angle 1.68538 ( 36) link_ALPHA1-6 : bond 0.00701 ( 9) link_ALPHA1-6 : angle 1.87687 ( 27) link_BETA1-4 : bond 0.00952 ( 24) link_BETA1-4 : angle 2.28670 ( 72) link_NAG-ASN : bond 0.00502 ( 33) link_NAG-ASN : angle 2.74611 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 635 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7571 (m-40) cc_final: 0.7282 (m110) REVERT: A 620 SER cc_start: 0.8370 (m) cc_final: 0.7897 (p) REVERT: A 624 ASP cc_start: 0.7889 (m-30) cc_final: 0.7408 (m-30) REVERT: B 528 SER cc_start: 0.9333 (p) cc_final: 0.9081 (m) REVERT: B 612 SER cc_start: 0.8702 (t) cc_final: 0.8262 (t) REVERT: B 620 SER cc_start: 0.8007 (m) cc_final: 0.7771 (p) REVERT: B 624 ASP cc_start: 0.7662 (m-30) cc_final: 0.7290 (m-30) REVERT: C 585 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7919 (tpp-160) REVERT: C 624 ASP cc_start: 0.7518 (m-30) cc_final: 0.7214 (m-30) REVERT: D 52 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8748 (mp) REVERT: D 92 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: D 358 ILE cc_start: 0.7408 (mm) cc_final: 0.7178 (mt) REVERT: D 430 ILE cc_start: 0.9071 (mm) cc_final: 0.8800 (mm) REVERT: D 484 TYR cc_start: 0.8613 (p90) cc_final: 0.8374 (p90) REVERT: F 64 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7496 (tm-30) REVERT: F 78 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7790 (t70) REVERT: G 32 ASN cc_start: 0.8469 (t0) cc_final: 0.8078 (t0) REVERT: G 40 GLN cc_start: 0.8570 (mt0) cc_final: 0.7936 (mt0) REVERT: G 60 SER cc_start: 0.9401 (p) cc_final: 0.9159 (p) REVERT: H 32 ASN cc_start: 0.8341 (t0) cc_final: 0.8087 (t0) REVERT: H 40 GLN cc_start: 0.8546 (mt0) cc_final: 0.8091 (mt0) REVERT: H 64 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8577 (mm-40) REVERT: J 32 ASP cc_start: 0.7814 (m-30) cc_final: 0.7506 (m-30) REVERT: J 37 GLN cc_start: 0.6734 (tt0) cc_final: 0.6442 (tt0) REVERT: J 90 GLN cc_start: 0.8537 (pp30) cc_final: 0.8246 (pp30) REVERT: K 3 GLN cc_start: 0.6961 (mp10) cc_final: 0.6705 (mp10) REVERT: K 12 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8099 (mmmt) REVERT: K 13 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7786 (mmtm) REVERT: K 19 LYS cc_start: 0.8677 (tptt) cc_final: 0.8398 (tptp) REVERT: K 67 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7281 (mtm110) REVERT: K 86 LEU cc_start: 0.8430 (mt) cc_final: 0.7885 (mt) REVERT: K 95 PHE cc_start: 0.8601 (m-80) cc_final: 0.8006 (m-80) REVERT: K 111 ASN cc_start: 0.8749 (t0) cc_final: 0.8271 (t0) REVERT: L 24 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7807 (tpp-160) REVERT: L 90 GLN cc_start: 0.7954 (pp30) cc_final: 0.7753 (pp30) REVERT: M 19 LYS cc_start: 0.8363 (tppt) cc_final: 0.7955 (tptp) REVERT: M 103 GLU cc_start: 0.6847 (pm20) cc_final: 0.6601 (pm20) REVERT: M 110 ASP cc_start: 0.7932 (m-30) cc_final: 0.7260 (t0) REVERT: N 23 CYS cc_start: 0.4409 (t) cc_final: 0.4158 (t) REVERT: N 53 THR cc_start: 0.8765 (t) cc_final: 0.8396 (p) REVERT: N 87 TYR cc_start: 0.7624 (m-80) cc_final: 0.7387 (m-80) REVERT: N 90 GLN cc_start: 0.8393 (pp30) cc_final: 0.8163 (pp30) REVERT: O 3 GLN cc_start: 0.7065 (mp10) cc_final: 0.6778 (mp10) REVERT: O 19 LYS cc_start: 0.8764 (tptt) cc_final: 0.8257 (tptt) REVERT: O 67 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7016 (ptm160) REVERT: O 85 ASN cc_start: 0.7487 (t0) cc_final: 0.7109 (t0) REVERT: O 86 LEU cc_start: 0.7930 (mt) cc_final: 0.6740 (mt) REVERT: O 87 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8014 (mmp-170) REVERT: O 101 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7486 (mm-30) REVERT: O 110 ASP cc_start: 0.8136 (m-30) cc_final: 0.7645 (t0) REVERT: O 111 ASN cc_start: 0.8522 (t0) cc_final: 0.7970 (t0) REVERT: P 13 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7545 (mmtt) REVERT: R 89 LEU cc_start: 0.8512 (tp) cc_final: 0.8260 (tp) REVERT: S 12 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8307 (t) REVERT: S 83 ASP cc_start: 0.7957 (m-30) cc_final: 0.7391 (m-30) REVERT: S 101 GLN cc_start: 0.7885 (mt0) cc_final: 0.7464 (mm-40) REVERT: U 4 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7326 (mtm) REVERT: U 6 GLN cc_start: 0.7878 (tt0) cc_final: 0.7418 (tt0) outliers start: 108 outliers final: 75 residues processed: 694 average time/residue: 0.1811 time to fit residues: 195.9423 Evaluate side-chains 690 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 609 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 4 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 0.3980 chunk 176 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN H 94 GLN I 32 ASN I 73 ASN I 94 GLN K 65 GLN K 120 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096859 restraints weight = 41460.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100192 restraints weight = 22180.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102354 restraints weight = 15013.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103706 restraints weight = 11750.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104585 restraints weight = 10078.834| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26124 Z= 0.141 Angle : 0.724 19.456 35700 Z= 0.355 Chirality : 0.048 0.452 4278 Planarity : 0.004 0.038 4350 Dihedral : 8.603 70.742 5178 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.77 % Allowed : 16.15 % Favored : 80.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.15), residues: 3099 helix: 0.35 (0.26), residues: 435 sheet: -0.93 (0.17), residues: 1032 loop : -1.98 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 84 TYR 0.033 0.002 TYR J 49 PHE 0.022 0.002 PHE K 114 TRP 0.065 0.001 TRP K 36 HIS 0.024 0.001 HIS K 63 Details of bonding type rmsd covalent geometry : bond 0.00318 (25986) covalent geometry : angle 0.69752 (35340) SS BOND : bond 0.00458 ( 45) SS BOND : angle 1.74779 ( 90) hydrogen bonds : bond 0.03585 ( 849) hydrogen bonds : angle 5.24018 ( 2349) Misc. bond : bond 0.00583 ( 3) link_ALPHA1-2 : bond 0.00572 ( 12) link_ALPHA1-2 : angle 1.86845 ( 36) link_ALPHA1-3 : bond 0.01019 ( 12) link_ALPHA1-3 : angle 1.66291 ( 36) link_ALPHA1-6 : bond 0.00665 ( 9) link_ALPHA1-6 : angle 1.95125 ( 27) link_BETA1-4 : bond 0.00833 ( 24) link_BETA1-4 : angle 2.15544 ( 72) link_NAG-ASN : bond 0.00496 ( 33) link_NAG-ASN : angle 2.47085 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 647 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7582 (m-40) cc_final: 0.7251 (m110) REVERT: A 620 SER cc_start: 0.8291 (m) cc_final: 0.7703 (p) REVERT: A 624 ASP cc_start: 0.7886 (m-30) cc_final: 0.7407 (m-30) REVERT: B 588 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7344 (ttt90) REVERT: B 612 SER cc_start: 0.8478 (t) cc_final: 0.8021 (t) REVERT: C 585 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7932 (tpp-160) REVERT: C 624 ASP cc_start: 0.7553 (m-30) cc_final: 0.7224 (m-30) REVERT: D 92 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: D 95 MET cc_start: 0.8734 (ptm) cc_final: 0.8379 (ttm) REVERT: D 358 ILE cc_start: 0.7327 (mm) cc_final: 0.7105 (mt) REVERT: D 430 ILE cc_start: 0.9082 (mm) cc_final: 0.8786 (mm) REVERT: D 484 TYR cc_start: 0.8591 (p90) cc_final: 0.8379 (p90) REVERT: E 78 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7981 (t70) REVERT: F 64 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7531 (tt0) REVERT: F 78 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7597 (t70) REVERT: G 32 ASN cc_start: 0.8446 (t0) cc_final: 0.8066 (t0) REVERT: G 40 GLN cc_start: 0.8560 (mt0) cc_final: 0.8057 (mt0) REVERT: H 32 ASN cc_start: 0.8332 (t0) cc_final: 0.8057 (t0) REVERT: H 40 GLN cc_start: 0.8506 (mt0) cc_final: 0.7859 (mt0) REVERT: H 64 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8534 (mm-40) REVERT: I 80 ASP cc_start: 0.7075 (m-30) cc_final: 0.6826 (m-30) REVERT: J 90 GLN cc_start: 0.8608 (pp30) cc_final: 0.8319 (pp30) REVERT: J 102 GLN cc_start: 0.7558 (mp10) cc_final: 0.7351 (mp10) REVERT: K 3 GLN cc_start: 0.6897 (mp10) cc_final: 0.6655 (mp10) REVERT: K 12 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7991 (mmmt) REVERT: K 13 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7955 (mmtm) REVERT: K 19 LYS cc_start: 0.8626 (tptt) cc_final: 0.8401 (tptp) REVERT: K 67 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7093 (mtm110) REVERT: K 85 ASN cc_start: 0.7147 (t0) cc_final: 0.6873 (t0) REVERT: K 86 LEU cc_start: 0.8307 (mt) cc_final: 0.7867 (mt) REVERT: K 111 ASN cc_start: 0.8691 (t0) cc_final: 0.8349 (t0) REVERT: L 24 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7697 (tpp-160) REVERT: L 90 GLN cc_start: 0.8017 (pp30) cc_final: 0.7816 (pp30) REVERT: M 19 LYS cc_start: 0.8406 (tppt) cc_final: 0.8033 (tptp) REVERT: M 101 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7038 (mm-30) REVERT: M 103 GLU cc_start: 0.6870 (pm20) cc_final: 0.6617 (pm20) REVERT: M 110 ASP cc_start: 0.7831 (m-30) cc_final: 0.7286 (t0) REVERT: N 53 THR cc_start: 0.8679 (t) cc_final: 0.8339 (p) REVERT: N 87 TYR cc_start: 0.7622 (m-80) cc_final: 0.7346 (m-80) REVERT: N 90 GLN cc_start: 0.8393 (pp30) cc_final: 0.8093 (pp30) REVERT: O 3 GLN cc_start: 0.7054 (mp10) cc_final: 0.6853 (mp10) REVERT: O 19 LYS cc_start: 0.8612 (tptt) cc_final: 0.8145 (tptt) REVERT: O 67 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6989 (ptm160) REVERT: O 85 ASN cc_start: 0.7417 (t0) cc_final: 0.7164 (t0) REVERT: O 86 LEU cc_start: 0.8024 (mt) cc_final: 0.6906 (mt) REVERT: O 87 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8017 (mmp-170) REVERT: O 101 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7436 (mm-30) REVERT: O 110 ASP cc_start: 0.8122 (m-30) cc_final: 0.7657 (t0) REVERT: O 111 ASN cc_start: 0.8525 (t0) cc_final: 0.7976 (t0) REVERT: O 116 LYS cc_start: 0.8750 (tptm) cc_final: 0.8397 (tmtt) REVERT: P 13 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7578 (mmtt) REVERT: R 89 LEU cc_start: 0.8507 (tp) cc_final: 0.8282 (tp) REVERT: S 12 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8311 (t) REVERT: S 83 ASP cc_start: 0.7879 (m-30) cc_final: 0.7403 (m-30) REVERT: S 101 GLN cc_start: 0.7849 (mt0) cc_final: 0.7383 (mm-40) REVERT: U 4 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7021 (mtm) REVERT: U 6 GLN cc_start: 0.7723 (tt0) cc_final: 0.7351 (tt0) REVERT: U 12 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8360 (t) outliers start: 99 outliers final: 69 residues processed: 706 average time/residue: 0.1786 time to fit residues: 195.3187 Evaluate side-chains 682 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 606 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 94 GLN I 32 ASN I 73 ASN I 94 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 111 ASN O 65 GLN Q 80 GLN ** T 6 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.129077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096085 restraints weight = 41385.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099388 restraints weight = 22446.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101537 restraints weight = 15311.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102894 restraints weight = 12034.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103674 restraints weight = 10342.543| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26124 Z= 0.162 Angle : 0.766 22.896 35700 Z= 0.374 Chirality : 0.050 0.526 4278 Planarity : 0.004 0.049 4350 Dihedral : 8.440 70.068 5178 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.08 % Allowed : 16.61 % Favored : 79.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.15), residues: 3099 helix: 0.49 (0.26), residues: 435 sheet: -0.78 (0.17), residues: 996 loop : -1.95 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 38 TYR 0.033 0.002 TYR J 49 PHE 0.021 0.002 PHE O 114 TRP 0.084 0.002 TRP K 36 HIS 0.003 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00368 (25986) covalent geometry : angle 0.74057 (35340) SS BOND : bond 0.00534 ( 45) SS BOND : angle 1.92724 ( 90) hydrogen bonds : bond 0.03609 ( 849) hydrogen bonds : angle 5.20355 ( 2349) Misc. bond : bond 0.01431 ( 3) link_ALPHA1-2 : bond 0.00908 ( 12) link_ALPHA1-2 : angle 1.92016 ( 36) link_ALPHA1-3 : bond 0.00810 ( 12) link_ALPHA1-3 : angle 1.86996 ( 36) link_ALPHA1-6 : bond 0.00608 ( 9) link_ALPHA1-6 : angle 1.99433 ( 27) link_BETA1-4 : bond 0.00834 ( 24) link_BETA1-4 : angle 2.16129 ( 72) link_NAG-ASN : bond 0.00502 ( 33) link_NAG-ASN : angle 2.33809 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 633 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7678 (m-40) cc_final: 0.7373 (m110) REVERT: A 620 SER cc_start: 0.8206 (m) cc_final: 0.7720 (p) REVERT: A 624 ASP cc_start: 0.7902 (m-30) cc_final: 0.7400 (m-30) REVERT: B 612 SER cc_start: 0.8562 (t) cc_final: 0.8071 (t) REVERT: C 585 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7791 (tpp-160) REVERT: C 624 ASP cc_start: 0.7582 (m-30) cc_final: 0.7249 (m-30) REVERT: D 92 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: D 358 ILE cc_start: 0.7344 (mm) cc_final: 0.7124 (mt) REVERT: D 430 ILE cc_start: 0.9149 (mm) cc_final: 0.8889 (mm) REVERT: D 435 TYR cc_start: 0.8721 (m-10) cc_final: 0.8474 (m-10) REVERT: E 78 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7865 (t70) REVERT: F 64 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7598 (tt0) REVERT: F 78 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7627 (t70) REVERT: G 32 ASN cc_start: 0.8489 (t0) cc_final: 0.8117 (t0) REVERT: G 40 GLN cc_start: 0.8581 (mt0) cc_final: 0.8078 (mt0) REVERT: H 32 ASN cc_start: 0.8406 (t0) cc_final: 0.8121 (t0) REVERT: H 40 GLN cc_start: 0.8546 (mt0) cc_final: 0.7965 (mt0) REVERT: H 64 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8545 (mm-40) REVERT: I 8 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8192 (ttpt) REVERT: I 40 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7994 (mm-40) REVERT: I 80 ASP cc_start: 0.6993 (m-30) cc_final: 0.6770 (m-30) REVERT: J 48 ILE cc_start: 0.7512 (mm) cc_final: 0.7308 (mm) REVERT: J 90 GLN cc_start: 0.8736 (pp30) cc_final: 0.8464 (pp30) REVERT: K 3 GLN cc_start: 0.7153 (mp10) cc_final: 0.6919 (mp10) REVERT: K 12 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8020 (mmmt) REVERT: K 13 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7962 (mmtm) REVERT: K 19 LYS cc_start: 0.8621 (tptt) cc_final: 0.8382 (tptp) REVERT: K 67 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7215 (mtm110) REVERT: K 85 ASN cc_start: 0.7036 (t0) cc_final: 0.6831 (t0) REVERT: K 86 LEU cc_start: 0.8383 (mt) cc_final: 0.7920 (mt) REVERT: K 101 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7427 (mm-30) REVERT: K 111 ASN cc_start: 0.8766 (t0) cc_final: 0.8276 (t0) REVERT: L 36 TYR cc_start: 0.7664 (m-80) cc_final: 0.7463 (m-10) REVERT: L 70 GLU cc_start: 0.6359 (tp30) cc_final: 0.6121 (tp30) REVERT: L 90 GLN cc_start: 0.8076 (pp30) cc_final: 0.7862 (pp30) REVERT: M 19 LYS cc_start: 0.8506 (tppt) cc_final: 0.7873 (tptp) REVERT: M 38 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6899 (ttm110) REVERT: M 103 GLU cc_start: 0.6885 (pm20) cc_final: 0.6634 (pm20) REVERT: M 111 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7562 (t0) REVERT: N 24 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7815 (mmm160) REVERT: N 48 ILE cc_start: 0.7640 (mm) cc_final: 0.7435 (mm) REVERT: N 53 THR cc_start: 0.8645 (t) cc_final: 0.8346 (p) REVERT: N 90 GLN cc_start: 0.8466 (pp30) cc_final: 0.8173 (pp30) REVERT: O 3 GLN cc_start: 0.7148 (mp10) cc_final: 0.6885 (mp10) REVERT: O 19 LYS cc_start: 0.8405 (tptt) cc_final: 0.7911 (tptt) REVERT: O 86 LEU cc_start: 0.7938 (mt) cc_final: 0.6655 (mt) REVERT: O 87 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.8042 (mmp-170) REVERT: O 101 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7432 (mm-30) REVERT: O 111 ASN cc_start: 0.8476 (t0) cc_final: 0.7902 (t0) REVERT: O 116 LYS cc_start: 0.8726 (tptm) cc_final: 0.8389 (tmtt) REVERT: P 13 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7562 (mmtt) REVERT: R 89 LEU cc_start: 0.8562 (tp) cc_final: 0.8330 (tp) REVERT: S 83 ASP cc_start: 0.7802 (m-30) cc_final: 0.7370 (m-30) REVERT: S 101 GLN cc_start: 0.7853 (mt0) cc_final: 0.7448 (mm-40) REVERT: U 6 GLN cc_start: 0.7629 (tt0) cc_final: 0.7268 (tt0) REVERT: U 12 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (t) outliers start: 107 outliers final: 81 residues processed: 691 average time/residue: 0.1881 time to fit residues: 201.8409 Evaluate side-chains 691 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 604 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 68 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 94 GLN I 32 ASN I 73 ASN I 94 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 120 GLN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 80 GLN ** T 6 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.128727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096222 restraints weight = 41516.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100037 restraints weight = 22741.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101455 restraints weight = 14923.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102656 restraints weight = 11410.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102862 restraints weight = 10358.666| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26124 Z= 0.169 Angle : 0.761 18.994 35700 Z= 0.370 Chirality : 0.049 0.503 4278 Planarity : 0.004 0.040 4350 Dihedral : 8.390 69.409 5178 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.73 % Allowed : 17.87 % Favored : 78.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.15), residues: 3099 helix: 0.62 (0.26), residues: 435 sheet: -0.71 (0.17), residues: 1008 loop : -1.93 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 20 TYR 0.033 0.002 TYR J 49 PHE 0.022 0.002 PHE K 114 TRP 0.092 0.002 TRP K 36 HIS 0.004 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00387 (25986) covalent geometry : angle 0.73325 (35340) SS BOND : bond 0.00532 ( 45) SS BOND : angle 2.00985 ( 90) hydrogen bonds : bond 0.03626 ( 849) hydrogen bonds : angle 5.17995 ( 2349) Misc. bond : bond 0.01215 ( 3) link_ALPHA1-2 : bond 0.00931 ( 12) link_ALPHA1-2 : angle 2.20367 ( 36) link_ALPHA1-3 : bond 0.00796 ( 12) link_ALPHA1-3 : angle 1.82648 ( 36) link_ALPHA1-6 : bond 0.00573 ( 9) link_ALPHA1-6 : angle 2.03236 ( 27) link_BETA1-4 : bond 0.00917 ( 24) link_BETA1-4 : angle 2.21684 ( 72) link_NAG-ASN : bond 0.00499 ( 33) link_NAG-ASN : angle 2.32850 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 640 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7675 (m-40) cc_final: 0.7373 (m110) REVERT: A 620 SER cc_start: 0.8261 (m) cc_final: 0.7811 (p) REVERT: A 624 ASP cc_start: 0.7882 (m-30) cc_final: 0.7378 (m-30) REVERT: B 612 SER cc_start: 0.8478 (t) cc_final: 0.8024 (t) REVERT: B 632 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8082 (t0) REVERT: C 585 ARG cc_start: 0.8036 (tpp80) cc_final: 0.7773 (tpp-160) REVERT: C 624 ASP cc_start: 0.7568 (m-30) cc_final: 0.7284 (m-30) REVERT: D 92 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: D 358 ILE cc_start: 0.7354 (mm) cc_final: 0.7144 (mt) REVERT: D 430 ILE cc_start: 0.9143 (mm) cc_final: 0.8879 (mm) REVERT: E 78 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7937 (t70) REVERT: F 78 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7484 (t70) REVERT: G 32 ASN cc_start: 0.8548 (t0) cc_final: 0.8175 (t0) REVERT: G 40 GLN cc_start: 0.8599 (mt0) cc_final: 0.8099 (mt0) REVERT: H 32 ASN cc_start: 0.8514 (t0) cc_final: 0.8247 (t0) REVERT: H 40 GLN cc_start: 0.8515 (mt0) cc_final: 0.7929 (mt0) REVERT: H 64 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8540 (mm-40) REVERT: I 8 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: I 80 ASP cc_start: 0.7074 (m-30) cc_final: 0.6861 (m-30) REVERT: J 90 GLN cc_start: 0.8846 (pp30) cc_final: 0.8264 (pp30) REVERT: K 3 GLN cc_start: 0.7169 (mp10) cc_final: 0.6942 (mp10) REVERT: K 12 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7809 (mmmt) REVERT: K 13 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7759 (mmtm) REVERT: K 19 LYS cc_start: 0.8566 (tptt) cc_final: 0.8337 (tptp) REVERT: K 67 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7250 (mtm110) REVERT: K 86 LEU cc_start: 0.8338 (mt) cc_final: 0.7822 (mt) REVERT: K 95 PHE cc_start: 0.8515 (m-80) cc_final: 0.8232 (m-80) REVERT: K 101 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7326 (mm-30) REVERT: K 111 ASN cc_start: 0.8772 (t0) cc_final: 0.8286 (t0) REVERT: L 36 TYR cc_start: 0.7748 (m-80) cc_final: 0.6939 (m-10) REVERT: L 90 GLN cc_start: 0.8081 (pp30) cc_final: 0.7867 (pp30) REVERT: M 19 LYS cc_start: 0.8518 (tppt) cc_final: 0.7850 (tptp) REVERT: M 101 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7005 (mm-30) REVERT: M 103 GLU cc_start: 0.7285 (pm20) cc_final: 0.6871 (pm20) REVERT: M 110 ASP cc_start: 0.8047 (m-30) cc_final: 0.7430 (t0) REVERT: M 111 ASN cc_start: 0.8081 (t0) cc_final: 0.7517 (t0) REVERT: N 36 TYR cc_start: 0.7498 (m-10) cc_final: 0.7250 (m-10) REVERT: N 53 THR cc_start: 0.8609 (t) cc_final: 0.8383 (p) REVERT: N 90 GLN cc_start: 0.8486 (pp30) cc_final: 0.8205 (pp30) REVERT: O 3 GLN cc_start: 0.7115 (mp10) cc_final: 0.6885 (mp10) REVERT: O 10 GLU cc_start: 0.6296 (tp30) cc_final: 0.6075 (mm-30) REVERT: O 19 LYS cc_start: 0.8377 (tptt) cc_final: 0.8002 (tptp) REVERT: O 67 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6810 (ptm160) REVERT: O 87 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7946 (tpp-160) REVERT: O 101 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7400 (mm-30) REVERT: O 111 ASN cc_start: 0.8482 (t0) cc_final: 0.7903 (t0) REVERT: O 116 LYS cc_start: 0.8682 (tptm) cc_final: 0.8346 (tmtt) REVERT: O 120 GLN cc_start: 0.7076 (mp10) cc_final: 0.6802 (mp10) REVERT: P 13 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7543 (mmtt) REVERT: R 89 LEU cc_start: 0.8645 (tp) cc_final: 0.8425 (tp) REVERT: S 83 ASP cc_start: 0.7669 (m-30) cc_final: 0.7247 (m-30) REVERT: S 101 GLN cc_start: 0.7847 (mt0) cc_final: 0.7440 (mm-40) REVERT: U 6 GLN cc_start: 0.7665 (tt0) cc_final: 0.7291 (tt0) REVERT: U 12 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8361 (t) REVERT: U 40 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7860 (mmm-85) REVERT: U 61 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8496 (t) outliers start: 98 outliers final: 80 residues processed: 695 average time/residue: 0.1801 time to fit residues: 194.3938 Evaluate side-chains 693 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 605 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 22 CYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 184 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 94 GLN I 94 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 HIS Q 78 ASN Q 80 GLN R 36 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095349 restraints weight = 41250.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098673 restraints weight = 22272.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100811 restraints weight = 15141.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102188 restraints weight = 11877.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103033 restraints weight = 10196.131| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26124 Z= 0.171 Angle : 0.822 23.549 35700 Z= 0.392 Chirality : 0.052 0.640 4278 Planarity : 0.004 0.045 4350 Dihedral : 8.466 69.124 5178 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 3.58 % Allowed : 18.25 % Favored : 78.17 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.15), residues: 3099 helix: 0.69 (0.26), residues: 435 sheet: -0.69 (0.17), residues: 1008 loop : -1.89 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 97 TYR 0.030 0.002 TYR J 49 PHE 0.023 0.002 PHE O 114 TRP 0.098 0.002 TRP K 36 HIS 0.004 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00384 (25986) covalent geometry : angle 0.79352 (35340) SS BOND : bond 0.00526 ( 45) SS BOND : angle 2.05291 ( 90) hydrogen bonds : bond 0.03587 ( 849) hydrogen bonds : angle 5.16134 ( 2349) Misc. bond : bond 0.02340 ( 3) link_ALPHA1-2 : bond 0.01142 ( 12) link_ALPHA1-2 : angle 3.05768 ( 36) link_ALPHA1-3 : bond 0.00949 ( 12) link_ALPHA1-3 : angle 2.14953 ( 36) link_ALPHA1-6 : bond 0.00548 ( 9) link_ALPHA1-6 : angle 2.04798 ( 27) link_BETA1-4 : bond 0.00898 ( 24) link_BETA1-4 : angle 2.20611 ( 72) link_NAG-ASN : bond 0.00472 ( 33) link_NAG-ASN : angle 2.27934 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 609 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7694 (m-40) cc_final: 0.7385 (m110) REVERT: A 620 SER cc_start: 0.8305 (m) cc_final: 0.7844 (p) REVERT: A 624 ASP cc_start: 0.7914 (m-30) cc_final: 0.7417 (m-30) REVERT: B 612 SER cc_start: 0.8398 (t) cc_final: 0.7947 (t) REVERT: B 632 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8172 (t0) REVERT: C 585 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7789 (tpp-160) REVERT: C 624 ASP cc_start: 0.7591 (m-30) cc_final: 0.7247 (m-30) REVERT: D 92 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: D 358 ILE cc_start: 0.7317 (mm) cc_final: 0.7107 (mt) REVERT: D 430 ILE cc_start: 0.9166 (mm) cc_final: 0.8912 (mm) REVERT: E 78 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7932 (t70) REVERT: F 64 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7652 (tt0) REVERT: F 78 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7489 (t70) REVERT: F 100 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (mtp) REVERT: G 32 ASN cc_start: 0.8474 (t0) cc_final: 0.8117 (t0) REVERT: G 40 GLN cc_start: 0.8589 (mt0) cc_final: 0.8069 (mt0) REVERT: H 32 ASN cc_start: 0.8515 (t0) cc_final: 0.8253 (t0) REVERT: H 40 GLN cc_start: 0.8522 (mt0) cc_final: 0.7922 (mt0) REVERT: H 64 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8554 (mm-40) REVERT: I 8 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8181 (ttpt) REVERT: I 40 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8114 (mm-40) REVERT: I 80 ASP cc_start: 0.7059 (m-30) cc_final: 0.6853 (m-30) REVERT: K 3 GLN cc_start: 0.7113 (mp10) cc_final: 0.6886 (mp10) REVERT: K 12 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7743 (mmmt) REVERT: K 13 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7796 (mmtm) REVERT: K 67 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7319 (mtm110) REVERT: K 86 LEU cc_start: 0.8301 (mt) cc_final: 0.7866 (mt) REVERT: K 95 PHE cc_start: 0.8481 (m-80) cc_final: 0.8233 (m-80) REVERT: K 101 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7323 (mm-30) REVERT: K 111 ASN cc_start: 0.8802 (t0) cc_final: 0.8344 (t0) REVERT: L 36 TYR cc_start: 0.7732 (m-80) cc_final: 0.7512 (m-10) REVERT: L 90 GLN cc_start: 0.8194 (pp30) cc_final: 0.7953 (pp30) REVERT: M 19 LYS cc_start: 0.8530 (tppt) cc_final: 0.7880 (tptp) REVERT: M 103 GLU cc_start: 0.7342 (pm20) cc_final: 0.6929 (pm20) REVERT: M 110 ASP cc_start: 0.8029 (m-30) cc_final: 0.7469 (t0) REVERT: N 53 THR cc_start: 0.8587 (t) cc_final: 0.8264 (p) REVERT: N 70 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7510 (pm20) REVERT: N 90 GLN cc_start: 0.8542 (pp30) cc_final: 0.8245 (pp30) REVERT: O 3 GLN cc_start: 0.7123 (mp10) cc_final: 0.6888 (mp10) REVERT: O 19 LYS cc_start: 0.8447 (tptt) cc_final: 0.8055 (tptp) REVERT: O 67 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6336 (ttt180) REVERT: O 85 ASN cc_start: 0.7542 (p0) cc_final: 0.6562 (p0) REVERT: O 86 LEU cc_start: 0.8031 (mt) cc_final: 0.6881 (mt) REVERT: O 87 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7914 (tpp-160) REVERT: O 101 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7400 (mm-30) REVERT: O 111 ASN cc_start: 0.8489 (t0) cc_final: 0.7920 (t0) REVERT: O 116 LYS cc_start: 0.8683 (tptm) cc_final: 0.8386 (tmtt) REVERT: O 120 GLN cc_start: 0.7098 (mp10) cc_final: 0.6799 (mp10) REVERT: P 13 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7552 (mmtt) REVERT: R 89 LEU cc_start: 0.8643 (tp) cc_final: 0.8436 (tp) REVERT: R 121 SER cc_start: 0.8854 (t) cc_final: 0.8540 (p) REVERT: S 83 ASP cc_start: 0.7669 (m-30) cc_final: 0.7254 (m-30) REVERT: S 101 GLN cc_start: 0.7788 (mt0) cc_final: 0.7409 (mm-40) REVERT: U 6 GLN cc_start: 0.7679 (tt0) cc_final: 0.7306 (tt0) REVERT: U 40 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7593 (mtt180) REVERT: U 61 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8456 (t) outliers start: 94 outliers final: 74 residues processed: 658 average time/residue: 0.1692 time to fit residues: 173.3464 Evaluate side-chains 680 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 598 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 173 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 294 optimal weight: 0.2980 chunk 262 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 94 GLN I 94 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 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 = 0.3697 r_free = 0.3697 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.096341 restraints weight = 41445.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099661 restraints weight = 22450.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101724 restraints weight = 15313.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103208 restraints weight = 12106.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104070 restraints weight = 10348.602| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26124 Z= 0.156 Angle : 0.832 36.203 35700 Z= 0.394 Chirality : 0.052 0.843 4278 Planarity : 0.004 0.043 4350 Dihedral : 8.372 71.010 5178 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 3.12 % Allowed : 18.78 % Favored : 78.10 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.15), residues: 3099 helix: 0.80 (0.26), residues: 435 sheet: -0.61 (0.17), residues: 1008 loop : -1.91 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 87 TYR 0.029 0.002 TYR J 49 PHE 0.025 0.002 PHE K 114 TRP 0.095 0.002 TRP K 36 HIS 0.005 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00346 (25986) covalent geometry : angle 0.80855 (35340) SS BOND : bond 0.00530 ( 45) SS BOND : angle 1.92359 ( 90) hydrogen bonds : bond 0.03553 ( 849) hydrogen bonds : angle 5.13138 ( 2349) Misc. bond : bond 0.02121 ( 3) link_ALPHA1-2 : bond 0.00930 ( 12) link_ALPHA1-2 : angle 2.35794 ( 36) link_ALPHA1-3 : bond 0.00961 ( 12) link_ALPHA1-3 : angle 1.98120 ( 36) link_ALPHA1-6 : bond 0.00592 ( 9) link_ALPHA1-6 : angle 2.07222 ( 27) link_BETA1-4 : bond 0.00866 ( 24) link_BETA1-4 : angle 2.12614 ( 72) link_NAG-ASN : bond 0.00455 ( 33) link_NAG-ASN : angle 2.20471 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 613 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7692 (m-40) cc_final: 0.7389 (m110) REVERT: A 620 SER cc_start: 0.8290 (m) cc_final: 0.7784 (p) REVERT: A 624 ASP cc_start: 0.7894 (m-30) cc_final: 0.7384 (m-30) REVERT: B 612 SER cc_start: 0.8514 (t) cc_final: 0.8145 (t) REVERT: B 632 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (t0) REVERT: C 585 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7777 (tpp-160) REVERT: C 624 ASP cc_start: 0.7588 (m-30) cc_final: 0.7300 (m-30) REVERT: D 92 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: D 358 ILE cc_start: 0.7298 (mm) cc_final: 0.7089 (mt) REVERT: D 430 ILE cc_start: 0.9152 (mm) cc_final: 0.8885 (mm) REVERT: E 78 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7986 (t70) REVERT: F 64 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7617 (tt0) REVERT: F 78 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7479 (t70) REVERT: F 100 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: G 32 ASN cc_start: 0.8473 (t0) cc_final: 0.8115 (t0) REVERT: G 40 GLN cc_start: 0.8576 (mt0) cc_final: 0.8067 (mt0) REVERT: H 32 ASN cc_start: 0.8517 (t0) cc_final: 0.8280 (t0) REVERT: H 40 GLN cc_start: 0.8487 (mt0) cc_final: 0.7908 (mt0) REVERT: H 64 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8551 (mm-40) REVERT: I 8 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: I 40 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8134 (mm-40) REVERT: J 24 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7918 (mmm160) REVERT: J 61 ARG cc_start: 0.4848 (ptt90) cc_final: 0.4541 (ptt90) REVERT: K 3 GLN cc_start: 0.7107 (mp10) cc_final: 0.6884 (mp10) REVERT: K 13 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7949 (mmmt) REVERT: K 67 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7325 (mtm110) REVERT: K 86 LEU cc_start: 0.8316 (mt) cc_final: 0.7877 (mt) REVERT: K 95 PHE cc_start: 0.8488 (m-80) cc_final: 0.8242 (m-80) REVERT: K 101 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7272 (mm-30) REVERT: K 109 TYR cc_start: 0.8190 (t80) cc_final: 0.7909 (t80) REVERT: K 111 ASN cc_start: 0.8770 (t0) cc_final: 0.8327 (t0) REVERT: L 53 THR cc_start: 0.8395 (t) cc_final: 0.8136 (p) REVERT: L 90 GLN cc_start: 0.8243 (pp30) cc_final: 0.8011 (pp30) REVERT: M 103 GLU cc_start: 0.7413 (pm20) cc_final: 0.7028 (pm20) REVERT: M 110 ASP cc_start: 0.7864 (m-30) cc_final: 0.7512 (t0) REVERT: M 120 GLN cc_start: 0.6281 (mp10) cc_final: 0.6044 (mm-40) REVERT: N 53 THR cc_start: 0.8547 (t) cc_final: 0.8318 (p) REVERT: O 3 GLN cc_start: 0.7093 (mp10) cc_final: 0.6857 (mp10) REVERT: O 19 LYS cc_start: 0.8352 (tptt) cc_final: 0.7935 (tptp) REVERT: O 67 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6295 (ttt180) REVERT: O 85 ASN cc_start: 0.7507 (p0) cc_final: 0.6726 (p0) REVERT: O 86 LEU cc_start: 0.8005 (mt) cc_final: 0.6876 (mt) REVERT: O 101 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7367 (mm-30) REVERT: O 111 ASN cc_start: 0.8482 (t0) cc_final: 0.7913 (t0) REVERT: O 116 LYS cc_start: 0.8685 (tptm) cc_final: 0.8398 (tmtt) REVERT: O 120 GLN cc_start: 0.7185 (mp10) cc_final: 0.6893 (mp10) REVERT: P 13 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7444 (mmtt) REVERT: R 121 SER cc_start: 0.8832 (t) cc_final: 0.8332 (p) REVERT: S 83 ASP cc_start: 0.7661 (m-30) cc_final: 0.7296 (m-30) REVERT: S 101 GLN cc_start: 0.7688 (mt0) cc_final: 0.7329 (mm-40) REVERT: U 6 GLN cc_start: 0.7575 (tt0) cc_final: 0.7206 (tt0) REVERT: U 40 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7800 (mtp180) outliers start: 82 outliers final: 70 residues processed: 658 average time/residue: 0.1755 time to fit residues: 179.7793 Evaluate side-chains 673 residues out of total 2727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 596 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 302 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 105 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 211 optimal weight: 0.0980 chunk 243 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN D 85 HIS ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 94 GLN I 32 ASN I 94 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN Q 80 GLN S 78 ASN S 80 GLN T 6 GLN T 62 HIS U 80 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098135 restraints weight = 41289.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101601 restraints weight = 22387.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103450 restraints weight = 14935.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104560 restraints weight = 11224.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104845 restraints weight = 10123.148| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26124 Z= 0.141 Angle : 0.780 22.901 35700 Z= 0.370 Chirality : 0.048 0.441 4278 Planarity : 0.004 0.046 4350 Dihedral : 7.982 65.696 5178 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 3.05 % Allowed : 19.54 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.15), residues: 3099 helix: 0.92 (0.26), residues: 435 sheet: -0.58 (0.18), residues: 966 loop : -1.85 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 67 TYR 0.032 0.002 TYR J 36 PHE 0.024 0.002 PHE N 71 TRP 0.096 0.002 TRP O 36 HIS 0.005 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00318 (25986) covalent geometry : angle 0.75478 (35340) SS BOND : bond 0.00528 ( 45) SS BOND : angle 2.00482 ( 90) hydrogen bonds : bond 0.03497 ( 849) hydrogen bonds : angle 5.05905 ( 2349) Misc. bond : bond 0.01216 ( 3) link_ALPHA1-2 : bond 0.00661 ( 12) link_ALPHA1-2 : angle 2.43843 ( 36) link_ALPHA1-3 : bond 0.00870 ( 12) link_ALPHA1-3 : angle 1.86737 ( 36) link_ALPHA1-6 : bond 0.00584 ( 9) link_ALPHA1-6 : angle 2.03796 ( 27) link_BETA1-4 : bond 0.00825 ( 24) link_BETA1-4 : angle 2.04245 ( 72) link_NAG-ASN : bond 0.00433 ( 33) link_NAG-ASN : angle 2.12185 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.41 seconds wall clock time: 96 minutes 14.72 seconds (5774.72 seconds total)