Starting phenix.real_space_refine on Thu Feb 5 20:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.map" model { file = "/net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o2t_70021/02_2026/9o2t_70021.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12348 2.51 5 N 3294 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19686 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3403 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3403 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3403 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 6 Chain: "F" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 3, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.58, per 1000 atoms: 0.23 Number of scatterers: 19686 At special positions: 0 Unit cell: (131.456, 140.608, 140.608, 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 132 16.00 O 3912 8.00 N 3294 7.00 C 12348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.60 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 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 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 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 445 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.45 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 7 " - " MAN G 8 " " MAN W 7 " - " MAN W 8 " " MAN Z 7 " - " MAN Z 8 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 7 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 4 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 7 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " " MAN W 4 " - " NAG W 5 " " MAN Z 4 " - " NAG Z 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG G 5 " - " GAL G 6 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG W 5 " - " GAL W 6 " " 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 Z 5 " - " GAL Z 6 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 332 " " NAG C 604 " - " ASN C 363 " " NAG C 605 " - " ASN C 448 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 133 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 363 " " NAG E 607 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN C 301 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN E 301 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 160 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 386 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 521.1 milliseconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 30 sheets defined 19.0% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.760A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.772A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.544A pdb=" N GLY A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.742A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.459A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.836A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.515A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.760A pdb=" N ALA C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.772A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 149 through 152 removed outlier: 3.543A pdb=" N GLY C 152 " --> pdb=" O ASP C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.742A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.386A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.001A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.576A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.570A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.759A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 98 through 115 removed outlier: 3.772A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 149 through 152 removed outlier: 3.544A pdb=" N GLY E 152 " --> pdb=" O ASP E 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 149 through 152' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.742A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.801A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.529A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.861A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.002A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.668A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.834A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.139A pdb=" N GLY A 324 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 325 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 465 through 470 current: chain 'H' and resid 100E through 100J Processing sheet with id=AA7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.947A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.001A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.669A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.834A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.139A pdb=" N GLY C 324 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 325 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 465 through 470 current: chain 'J' and resid 100E through 100J Processing sheet with id=AB4, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.842A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.002A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.669A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.834A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.138A pdb=" N GLY E 324 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 325 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 465 through 470 current: chain 'M' and resid 100E through 100J Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.712A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.713A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.718A pdb=" N SER K 72 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.588A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU K 46 " --> pdb=" O ARG K 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.718A pdb=" N SER L 72 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.587A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'M' and resid 57 through 59 removed outlier: 5.712A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.717A pdb=" N SER N 72 " --> pdb=" O ALA N 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.586A pdb=" N VAL N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1512 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: 2.67 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6097 1.34 - 1.46: 5014 1.46 - 1.59: 8782 1.59 - 1.72: 0 1.72 - 1.84: 180 Bond restraints: 20073 Sorted by residual: bond pdb=" CA SER H 32 " pdb=" CB SER H 32 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.49e-02 4.50e+03 1.13e+01 bond pdb=" CA SER M 32 " pdb=" CB SER M 32 " ideal model delta sigma weight residual 1.527 1.478 0.050 1.49e-02 4.50e+03 1.11e+01 bond pdb=" CA SER J 32 " pdb=" CB SER J 32 " ideal model delta sigma weight residual 1.527 1.478 0.050 1.49e-02 4.50e+03 1.11e+01 bond pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.13e-02 7.83e+03 7.12e+00 bond pdb=" N TYR N 94 " pdb=" CA TYR N 94 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.13e-02 7.83e+03 7.10e+00 ... (remaining 20068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 26606 2.49 - 4.97: 563 4.97 - 7.46: 35 7.46 - 9.95: 18 9.95 - 12.43: 12 Bond angle restraints: 27234 Sorted by residual: angle pdb=" CA CYS E 445 " pdb=" CB CYS E 445 " pdb=" SG CYS E 445 " ideal model delta sigma weight residual 114.40 126.83 -12.43 2.30e+00 1.89e-01 2.92e+01 angle pdb=" CA CYS A 445 " pdb=" CB CYS A 445 " pdb=" SG CYS A 445 " ideal model delta sigma weight residual 114.40 126.80 -12.40 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CA CYS C 445 " pdb=" CB CYS C 445 " pdb=" SG CYS C 445 " ideal model delta sigma weight residual 114.40 126.78 -12.38 2.30e+00 1.89e-01 2.90e+01 angle pdb=" CA PHE H 100K" pdb=" CB PHE H 100K" pdb=" CG PHE H 100K" ideal model delta sigma weight residual 113.80 118.60 -4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" CA PHE M 100K" pdb=" CB PHE M 100K" pdb=" CG PHE M 100K" ideal model delta sigma weight residual 113.80 118.59 -4.79 1.00e+00 1.00e+00 2.29e+01 ... (remaining 27229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12406 22.64 - 45.28: 565 45.28 - 67.93: 117 67.93 - 90.57: 46 90.57 - 113.21: 36 Dihedral angle restraints: 13170 sinusoidal: 6399 harmonic: 6771 Sorted by residual: dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -3.67 -82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -4.09 -81.91 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -5.66 -80.34 1 1.00e+01 1.00e-02 7.99e+01 ... (remaining 13167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 3255 0.165 - 0.329: 57 0.329 - 0.494: 12 0.494 - 0.658: 0 0.658 - 0.823: 6 Chirality restraints: 3330 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.71 0.69 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 MAN Z 4 " pdb=" O6 BMA Z 3 " pdb=" C2 MAN Z 4 " pdb=" O5 MAN Z 4 " both_signs ideal model delta sigma weight residual False 2.40 1.72 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 MAN W 4 " pdb=" O6 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 1.72 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 3327 not shown) Planarity restraints: 3369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C7 NAG V 1 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.137 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C7 NAG Y 1 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.183 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.137 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C7 NAG I 1 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.183 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 3366 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 3 1.82 - 2.59: 201 2.59 - 3.36: 23063 3.36 - 4.13: 49569 4.13 - 4.90: 90607 Nonbonded interactions: 163443 Sorted by model distance: nonbonded pdb=" O ALA E 73 " pdb=" CD1 TRP F 571 " model vdw 1.052 3.260 nonbonded pdb=" O ALA E 73 " pdb=" CG TRP F 571 " model vdw 1.138 3.260 nonbonded pdb=" C ALA E 73 " pdb=" CD1 TRP F 571 " model vdw 1.656 3.490 nonbonded pdb=" OG SER F 528 " pdb=" O7 NAG E 601 " model vdw 1.851 3.040 nonbonded pdb=" O ILE C 491 " pdb=" NH2 ARG D 585 " model vdw 1.951 3.120 ... (remaining 163438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 16.470 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.008 0.570 20205 Z= 0.396 Angle : 0.940 13.849 27588 Z= 0.444 Chirality : 0.070 0.823 3330 Planarity : 0.007 0.114 3327 Dihedral : 14.759 113.210 8670 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2295 helix: -1.55 (0.24), residues: 426 sheet: -0.60 (0.20), residues: 693 loop : -1.01 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 444 TYR 0.023 0.002 TYR N 49 PHE 0.026 0.002 PHE J 100K TRP 0.015 0.001 TRP J 34 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00628 (20073) covalent geometry : angle 0.82593 (27234) SS BOND : bond 0.10916 ( 42) SS BOND : angle 3.77408 ( 84) hydrogen bonds : bond 0.24641 ( 567) hydrogen bonds : angle 8.98367 ( 1512) link_ALPHA1-2 : bond 0.00591 ( 3) link_ALPHA1-2 : angle 3.40377 ( 9) link_ALPHA1-3 : bond 0.02058 ( 9) link_ALPHA1-3 : angle 6.52583 ( 27) link_ALPHA1-6 : bond 0.00356 ( 6) link_ALPHA1-6 : angle 3.57750 ( 18) link_BETA1-2 : bond 0.00284 ( 3) link_BETA1-2 : angle 3.53500 ( 9) link_BETA1-4 : bond 0.01684 ( 27) link_BETA1-4 : angle 4.52275 ( 81) link_NAG-ASN : bond 0.00925 ( 42) link_NAG-ASN : angle 3.27875 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 671 time to evaluate : 0.670 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: B 612 SER cc_start: 0.8652 (m) cc_final: 0.8284 (t) REVERT: B 648 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 656 ASN cc_start: 0.9025 (m-40) cc_final: 0.8775 (m-40) REVERT: C 325 ASP cc_start: 0.6750 (t0) cc_final: 0.6486 (t0) REVERT: D 535 MET cc_start: 0.8365 (mmp) cc_final: 0.7869 (mmm) REVERT: D 612 SER cc_start: 0.8951 (m) cc_final: 0.8731 (t) REVERT: D 634 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7386 (mt-10) REVERT: D 638 TYR cc_start: 0.8262 (m-80) cc_final: 0.7945 (m-10) REVERT: D 647 GLU cc_start: 0.7724 (tt0) cc_final: 0.7298 (tt0) REVERT: D 657 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7740 (tp30) REVERT: E 107 ASP cc_start: 0.7500 (m-30) cc_final: 0.7056 (m-30) REVERT: E 375 SER cc_start: 0.8760 (t) cc_final: 0.8551 (p) REVERT: E 475 MET cc_start: 0.8558 (tpp) cc_final: 0.8294 (tpp) REVERT: F 634 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7697 (tt0) REVERT: H 36 TRP cc_start: 0.6975 (m100) cc_final: 0.6204 (m100) REVERT: H 38 ARG cc_start: 0.6092 (ptp-170) cc_final: 0.5710 (ptm160) REVERT: H 47 TRP cc_start: 0.8131 (t60) cc_final: 0.7584 (t60) REVERT: J 38 ARG cc_start: 0.6276 (ptp-170) cc_final: 0.5796 (ptm160) REVERT: K 34 SER cc_start: 0.7326 (p) cc_final: 0.7097 (p) REVERT: K 63 SER cc_start: 0.7749 (t) cc_final: 0.7204 (m) REVERT: K 82 ASP cc_start: 0.6810 (m-30) cc_final: 0.5987 (m-30) REVERT: L 5 THR cc_start: 0.8411 (m) cc_final: 0.7607 (t) REVERT: L 63 SER cc_start: 0.7855 (t) cc_final: 0.7309 (m) REVERT: L 82 ASP cc_start: 0.6368 (m-30) cc_final: 0.5533 (m-30) REVERT: N 5 THR cc_start: 0.7950 (m) cc_final: 0.7089 (t) REVERT: N 63 SER cc_start: 0.7519 (t) cc_final: 0.6967 (m) REVERT: N 79 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7763 (mm110) outliers start: 3 outliers final: 0 residues processed: 674 average time/residue: 0.1513 time to fit residues: 149.8557 Evaluate side-chains 406 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN C 103 GLN C 195 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 422 GLN C 425 ASN D 625 ASN D 653 GLN E 103 GLN E 137 ASN E 195 ASN E 411 ASN F 625 ASN F 653 GLN F 658 GLN H 57 HIS K 38 GLN L 38 GLN M 57 HIS N 3 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112197 restraints weight = 30758.094| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.67 r_work: 0.3238 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 20205 Z= 0.160 Angle : 0.720 10.804 27588 Z= 0.345 Chirality : 0.048 0.302 3330 Planarity : 0.005 0.054 3327 Dihedral : 10.226 81.366 4344 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.03 % Allowed : 11.21 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2295 helix: -0.18 (0.26), residues: 429 sheet: -0.35 (0.21), residues: 672 loop : -0.88 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 100J TYR 0.025 0.002 TYR L 49 PHE 0.015 0.001 PHE A 382 TRP 0.036 0.001 TRP F 571 HIS 0.011 0.001 HIS M 53 Details of bonding type rmsd covalent geometry : bond 0.00375 (20073) covalent geometry : angle 0.67159 (27234) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.98917 ( 84) hydrogen bonds : bond 0.04950 ( 567) hydrogen bonds : angle 5.85969 ( 1512) link_ALPHA1-2 : bond 0.00102 ( 3) link_ALPHA1-2 : angle 1.53611 ( 9) link_ALPHA1-3 : bond 0.01081 ( 9) link_ALPHA1-3 : angle 4.60198 ( 27) link_ALPHA1-6 : bond 0.00953 ( 6) link_ALPHA1-6 : angle 1.51529 ( 18) link_BETA1-2 : bond 0.00794 ( 3) link_BETA1-2 : angle 1.96869 ( 9) link_BETA1-4 : bond 0.00634 ( 27) link_BETA1-4 : angle 2.51774 ( 81) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 2.00112 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 428 time to evaluate : 0.509 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 91 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: A 370 GLU cc_start: 0.7991 (mp0) cc_final: 0.7602 (tt0) REVERT: A 411 ASN cc_start: 0.4304 (OUTLIER) cc_final: 0.4001 (m110) REVERT: B 542 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7514 (mtm-85) REVERT: B 612 SER cc_start: 0.8685 (m) cc_final: 0.8295 (t) REVERT: B 656 ASN cc_start: 0.8926 (m-40) cc_final: 0.8535 (m-40) REVERT: C 103 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: C 232 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8779 (mmmm) REVERT: D 535 MET cc_start: 0.8628 (mmp) cc_final: 0.8247 (mmm) REVERT: D 612 SER cc_start: 0.8969 (m) cc_final: 0.8752 (t) REVERT: D 617 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7217 (mtt180) REVERT: D 638 TYR cc_start: 0.8439 (m-80) cc_final: 0.8182 (m-10) REVERT: D 647 GLU cc_start: 0.8030 (tt0) cc_final: 0.7500 (tt0) REVERT: D 652 GLN cc_start: 0.8393 (tt0) cc_final: 0.8010 (tt0) REVERT: D 653 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: D 656 ASN cc_start: 0.8968 (m-40) cc_final: 0.8544 (m110) REVERT: D 657 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7770 (tp30) REVERT: E 188 ASN cc_start: 0.7044 (p0) cc_final: 0.6768 (p0) REVERT: E 375 SER cc_start: 0.8943 (t) cc_final: 0.8738 (p) REVERT: F 542 ARG cc_start: 0.8885 (ttp-170) cc_final: 0.8199 (mtm-85) REVERT: F 605 CYS cc_start: 0.7588 (m) cc_final: 0.7324 (m) REVERT: F 608 VAL cc_start: 0.9123 (t) cc_final: 0.8918 (p) REVERT: F 632 ASP cc_start: 0.8594 (t0) cc_final: 0.8380 (t0) REVERT: F 647 GLU cc_start: 0.8072 (tt0) cc_final: 0.7761 (tt0) REVERT: H 36 TRP cc_start: 0.6944 (m100) cc_final: 0.5618 (m100) REVERT: H 38 ARG cc_start: 0.6046 (ptp-170) cc_final: 0.5579 (ptm160) REVERT: J 38 ARG cc_start: 0.6136 (ptp-170) cc_final: 0.5219 (tmm160) REVERT: J 67 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6272 (mm) REVERT: J 91 TYR cc_start: 0.7756 (m-80) cc_final: 0.7379 (m-80) REVERT: K 82 ASP cc_start: 0.7567 (m-30) cc_final: 0.6941 (m-30) REVERT: L 82 ASP cc_start: 0.7166 (m-30) cc_final: 0.6452 (m-30) REVERT: N 79 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7895 (mm110) outliers start: 62 outliers final: 29 residues processed: 470 average time/residue: 0.1345 time to fit residues: 96.4435 Evaluate side-chains 403 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 369 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 179 optimal weight: 0.0270 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS C 195 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN E 103 GLN E 137 ASN E 195 ASN E 411 ASN E 422 GLN H 57 HIS J 57 HIS L 38 GLN M 57 HIS M 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108818 restraints weight = 30834.494| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.87 r_work: 0.3209 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20205 Z= 0.163 Angle : 0.675 8.653 27588 Z= 0.322 Chirality : 0.047 0.270 3330 Planarity : 0.004 0.050 3327 Dihedral : 9.457 78.355 4344 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.52 % Allowed : 14.15 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2295 helix: 0.26 (0.26), residues: 429 sheet: -0.73 (0.20), residues: 729 loop : -0.83 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.024 0.002 TYR L 49 PHE 0.011 0.001 PHE A 382 TRP 0.037 0.001 TRP K 35 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00381 (20073) covalent geometry : angle 0.63164 (27234) SS BOND : bond 0.00754 ( 42) SS BOND : angle 1.64692 ( 84) hydrogen bonds : bond 0.04187 ( 567) hydrogen bonds : angle 5.39077 ( 1512) link_ALPHA1-2 : bond 0.00055 ( 3) link_ALPHA1-2 : angle 1.78082 ( 9) link_ALPHA1-3 : bond 0.01018 ( 9) link_ALPHA1-3 : angle 4.18758 ( 27) link_ALPHA1-6 : bond 0.00997 ( 6) link_ALPHA1-6 : angle 1.24802 ( 18) link_BETA1-2 : bond 0.00308 ( 3) link_BETA1-2 : angle 2.05763 ( 9) link_BETA1-4 : bond 0.00490 ( 27) link_BETA1-4 : angle 2.30442 ( 81) link_NAG-ASN : bond 0.00248 ( 42) link_NAG-ASN : angle 1.93468 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 410 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7973 (tt0) cc_final: 0.7270 (tm-30) REVERT: B 542 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.7795 (mtm-85) REVERT: B 612 SER cc_start: 0.8712 (m) cc_final: 0.8436 (t) REVERT: C 103 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8630 (tp-100) REVERT: C 232 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8827 (mmtp) REVERT: D 535 MET cc_start: 0.8722 (mmp) cc_final: 0.8463 (mmm) REVERT: D 585 ARG cc_start: 0.8736 (ttp80) cc_final: 0.8501 (mtp85) REVERT: D 612 SER cc_start: 0.8974 (m) cc_final: 0.8738 (t) REVERT: D 617 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7930 (mtt180) REVERT: D 646 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8790 (mm) REVERT: D 647 GLU cc_start: 0.8144 (tt0) cc_final: 0.7732 (tt0) REVERT: D 652 GLN cc_start: 0.8665 (tt0) cc_final: 0.8249 (tt0) REVERT: D 653 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: D 656 ASN cc_start: 0.8853 (m-40) cc_final: 0.8398 (m110) REVERT: D 657 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7821 (tp30) REVERT: E 153 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: E 188 ASN cc_start: 0.7234 (p0) cc_final: 0.6955 (p0) REVERT: E 375 SER cc_start: 0.9036 (t) cc_final: 0.8817 (p) REVERT: F 542 ARG cc_start: 0.8981 (ttp-170) cc_final: 0.8745 (ttm110) REVERT: F 605 CYS cc_start: 0.7614 (m) cc_final: 0.7265 (m) REVERT: F 608 VAL cc_start: 0.9238 (t) cc_final: 0.8994 (p) REVERT: F 647 GLU cc_start: 0.8275 (tt0) cc_final: 0.7978 (tt0) REVERT: H 18 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5990 (mm) REVERT: H 36 TRP cc_start: 0.6750 (m100) cc_final: 0.6147 (m100) REVERT: H 38 ARG cc_start: 0.5820 (ptp-170) cc_final: 0.5303 (tmm160) REVERT: J 38 ARG cc_start: 0.5998 (ptp-170) cc_final: 0.5579 (tmm160) REVERT: J 67 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6355 (mm) REVERT: J 91 TYR cc_start: 0.7674 (m-80) cc_final: 0.7191 (m-80) REVERT: L 88 CYS cc_start: 0.5499 (p) cc_final: 0.5180 (p) REVERT: M 67 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6098 (mm) REVERT: N 79 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7962 (mm110) outliers start: 72 outliers final: 45 residues processed: 452 average time/residue: 0.1223 time to fit residues: 84.0542 Evaluate side-chains 416 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 171 optimal weight: 0.0020 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN E 137 ASN E 411 ASN H 57 HIS J 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108238 restraints weight = 30949.000| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.64 r_work: 0.3187 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20205 Z= 0.144 Angle : 0.642 8.576 27588 Z= 0.306 Chirality : 0.045 0.260 3330 Planarity : 0.004 0.055 3327 Dihedral : 8.579 72.668 4344 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.87 % Allowed : 14.44 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2295 helix: 0.60 (0.27), residues: 429 sheet: -0.69 (0.20), residues: 729 loop : -0.87 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 24 TYR 0.021 0.001 TYR D 638 PHE 0.009 0.001 PHE C 159 TRP 0.028 0.001 TRP K 35 HIS 0.007 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00337 (20073) covalent geometry : angle 0.59862 (27234) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.60080 ( 84) hydrogen bonds : bond 0.03704 ( 567) hydrogen bonds : angle 5.10381 ( 1512) link_ALPHA1-2 : bond 0.00068 ( 3) link_ALPHA1-2 : angle 1.69563 ( 9) link_ALPHA1-3 : bond 0.01059 ( 9) link_ALPHA1-3 : angle 4.22816 ( 27) link_ALPHA1-6 : bond 0.00967 ( 6) link_ALPHA1-6 : angle 1.16421 ( 18) link_BETA1-2 : bond 0.00366 ( 3) link_BETA1-2 : angle 1.99161 ( 9) link_BETA1-4 : bond 0.00464 ( 27) link_BETA1-4 : angle 2.21066 ( 81) link_NAG-ASN : bond 0.00217 ( 42) link_NAG-ASN : angle 1.84495 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 404 time to evaluate : 0.761 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 103 GLN cc_start: 0.8011 (tt0) cc_final: 0.7427 (tm-30) REVERT: A 370 GLU cc_start: 0.8287 (mp0) cc_final: 0.7875 (tt0) REVERT: B 542 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7808 (mtm-85) REVERT: B 612 SER cc_start: 0.8705 (m) cc_final: 0.8461 (t) REVERT: D 647 GLU cc_start: 0.8051 (tt0) cc_final: 0.7681 (tt0) REVERT: D 652 GLN cc_start: 0.8640 (tt0) cc_final: 0.8241 (tt0) REVERT: D 653 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: D 656 ASN cc_start: 0.8872 (m-40) cc_final: 0.8431 (m110) REVERT: D 657 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7902 (tp30) REVERT: E 153 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: E 188 ASN cc_start: 0.7223 (p0) cc_final: 0.7004 (p0) REVERT: F 542 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8685 (ttm110) REVERT: F 605 CYS cc_start: 0.7547 (m) cc_final: 0.7210 (m) REVERT: F 617 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7824 (mtt180) REVERT: F 647 GLU cc_start: 0.8146 (tt0) cc_final: 0.7857 (tt0) REVERT: H 18 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6141 (mm) REVERT: H 38 ARG cc_start: 0.5792 (ptp-170) cc_final: 0.5408 (tmm160) REVERT: J 38 ARG cc_start: 0.6218 (ptp-170) cc_final: 0.5857 (tmm160) REVERT: J 67 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6183 (mm) REVERT: J 91 TYR cc_start: 0.7787 (m-80) cc_final: 0.7431 (m-80) REVERT: M 67 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6190 (mm) REVERT: N 79 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7861 (mm110) outliers start: 79 outliers final: 53 residues processed: 453 average time/residue: 0.1361 time to fit residues: 93.5496 Evaluate side-chains 429 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 371 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 222 optimal weight: 0.1980 chunk 131 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN C 188 ASN C 195 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN D 653 GLN E 137 ASN E 411 ASN H 57 HIS K 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103290 restraints weight = 31019.575| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.62 r_work: 0.3096 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 20205 Z= 0.271 Angle : 0.736 7.326 27588 Z= 0.354 Chirality : 0.048 0.249 3330 Planarity : 0.005 0.053 3327 Dihedral : 8.676 75.491 4344 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.41 % Allowed : 15.81 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2295 helix: 0.43 (0.27), residues: 429 sheet: -0.77 (0.19), residues: 759 loop : -0.96 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.023 0.002 TYR A 191 PHE 0.015 0.002 PHE A 159 TRP 0.028 0.002 TRP K 35 HIS 0.007 0.002 HIS M 53 Details of bonding type rmsd covalent geometry : bond 0.00652 (20073) covalent geometry : angle 0.69197 (27234) SS BOND : bond 0.00657 ( 42) SS BOND : angle 1.80564 ( 84) hydrogen bonds : bond 0.04132 ( 567) hydrogen bonds : angle 5.19267 ( 1512) link_ALPHA1-2 : bond 0.00155 ( 3) link_ALPHA1-2 : angle 1.76065 ( 9) link_ALPHA1-3 : bond 0.00925 ( 9) link_ALPHA1-3 : angle 4.00488 ( 27) link_ALPHA1-6 : bond 0.00802 ( 6) link_ALPHA1-6 : angle 0.94882 ( 18) link_BETA1-2 : bond 0.00496 ( 3) link_BETA1-2 : angle 1.98457 ( 9) link_BETA1-4 : bond 0.00452 ( 27) link_BETA1-4 : angle 2.36927 ( 81) link_NAG-ASN : bond 0.00422 ( 42) link_NAG-ASN : angle 2.31385 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 382 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8159 (tt0) cc_final: 0.7389 (tm-30) REVERT: B 574 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8029 (ttmt) REVERT: B 612 SER cc_start: 0.8769 (m) cc_final: 0.8540 (t) REVERT: C 116 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7570 (mp) REVERT: C 163 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 474 ASP cc_start: 0.7303 (t0) cc_final: 0.7039 (p0) REVERT: C 475 MET cc_start: 0.8630 (tpp) cc_final: 0.8321 (tpp) REVERT: D 535 MET cc_start: 0.8820 (mmm) cc_final: 0.8548 (mtt) REVERT: D 574 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8184 (ttmt) REVERT: D 646 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8909 (mm) REVERT: D 647 GLU cc_start: 0.8108 (tt0) cc_final: 0.7737 (tt0) REVERT: D 652 GLN cc_start: 0.8703 (tt0) cc_final: 0.8278 (tt0) REVERT: D 653 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: D 656 ASN cc_start: 0.8877 (m-40) cc_final: 0.8433 (m110) REVERT: D 657 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7826 (tp30) REVERT: E 116 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7180 (mp) REVERT: E 153 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: F 542 ARG cc_start: 0.8892 (ttp-170) cc_final: 0.8688 (ttm110) REVERT: F 605 CYS cc_start: 0.7634 (m) cc_final: 0.7228 (m) REVERT: F 616 ASN cc_start: 0.8549 (m110) cc_final: 0.8289 (m-40) REVERT: F 617 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7914 (mtt180) REVERT: H 18 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6089 (mm) REVERT: J 38 ARG cc_start: 0.6057 (ptp-170) cc_final: 0.5774 (tmm160) REVERT: J 67 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6180 (mm) REVERT: K 93 SER cc_start: 0.8282 (m) cc_final: 0.7859 (p) REVERT: L 86 TYR cc_start: 0.7871 (m-80) cc_final: 0.7507 (m-80) REVERT: M 18 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5513 (mm) REVERT: N 79 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7929 (mm110) REVERT: N 86 TYR cc_start: 0.7645 (m-80) cc_final: 0.7040 (m-80) REVERT: N 96 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7820 (mmt-90) outliers start: 90 outliers final: 61 residues processed: 444 average time/residue: 0.1578 time to fit residues: 105.5514 Evaluate side-chains 414 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 205 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105981 restraints weight = 30745.800| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.66 r_work: 0.3145 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20205 Z= 0.134 Angle : 0.646 7.680 27588 Z= 0.310 Chirality : 0.046 0.244 3330 Planarity : 0.004 0.054 3327 Dihedral : 7.974 66.855 4344 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.06 % Allowed : 16.74 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2295 helix: 0.74 (0.27), residues: 429 sheet: -0.66 (0.19), residues: 756 loop : -0.95 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.023 0.001 TYR L 49 PHE 0.009 0.001 PHE E 159 TRP 0.032 0.001 TRP K 35 HIS 0.008 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00310 (20073) covalent geometry : angle 0.60655 (27234) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.54056 ( 84) hydrogen bonds : bond 0.03560 ( 567) hydrogen bonds : angle 4.95468 ( 1512) link_ALPHA1-2 : bond 0.00068 ( 3) link_ALPHA1-2 : angle 1.73806 ( 9) link_ALPHA1-3 : bond 0.01282 ( 9) link_ALPHA1-3 : angle 3.80407 ( 27) link_ALPHA1-6 : bond 0.01050 ( 6) link_ALPHA1-6 : angle 0.96785 ( 18) link_BETA1-2 : bond 0.00359 ( 3) link_BETA1-2 : angle 2.00302 ( 9) link_BETA1-4 : bond 0.00396 ( 27) link_BETA1-4 : angle 2.15285 ( 81) link_NAG-ASN : bond 0.00223 ( 42) link_NAG-ASN : angle 1.87942 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 374 time to evaluate : 0.742 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 103 GLN cc_start: 0.8065 (tt0) cc_final: 0.7419 (tm-30) REVERT: A 296 CYS cc_start: 0.5565 (m) cc_final: 0.5308 (m) REVERT: C 166 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8440 (ttp80) REVERT: C 296 CYS cc_start: 0.5561 (m) cc_final: 0.5351 (m) REVERT: C 474 ASP cc_start: 0.7206 (t0) cc_final: 0.6999 (p0) REVERT: D 574 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8211 (ttmt) REVERT: D 646 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8840 (mm) REVERT: D 647 GLU cc_start: 0.8042 (tt0) cc_final: 0.7708 (tt0) REVERT: D 652 GLN cc_start: 0.8634 (tt0) cc_final: 0.8243 (tt0) REVERT: D 653 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: D 656 ASN cc_start: 0.8862 (m-40) cc_final: 0.8436 (m110) REVERT: D 657 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7951 (tp30) REVERT: E 153 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: F 605 CYS cc_start: 0.7550 (m) cc_final: 0.7128 (m) REVERT: F 656 ASN cc_start: 0.8718 (m-40) cc_final: 0.8086 (m110) REVERT: H 18 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6128 (mm) REVERT: H 38 ARG cc_start: 0.6567 (ttp80) cc_final: 0.6190 (tmm160) REVERT: J 29 LEU cc_start: 0.8671 (mm) cc_final: 0.8458 (mt) REVERT: J 67 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6082 (mm) REVERT: K 93 SER cc_start: 0.8012 (m) cc_final: 0.7805 (p) REVERT: L 86 TYR cc_start: 0.7781 (m-80) cc_final: 0.7440 (m-80) REVERT: M 67 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6412 (mm) REVERT: N 2 ILE cc_start: 0.7388 (mp) cc_final: 0.7165 (mp) REVERT: N 3 GLN cc_start: 0.8660 (mp10) cc_final: 0.8261 (mp10) REVERT: N 79 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7858 (mm110) outliers start: 83 outliers final: 56 residues processed: 433 average time/residue: 0.1580 time to fit residues: 103.7868 Evaluate side-chains 405 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 133 optimal weight: 0.1980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN E 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104220 restraints weight = 31079.785| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.66 r_work: 0.3107 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20205 Z= 0.201 Angle : 0.681 7.727 27588 Z= 0.326 Chirality : 0.046 0.236 3330 Planarity : 0.004 0.055 3327 Dihedral : 7.893 66.864 4344 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.82 % Allowed : 17.28 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2295 helix: 0.74 (0.27), residues: 429 sheet: -0.69 (0.19), residues: 756 loop : -0.99 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 542 TYR 0.026 0.002 TYR F 638 PHE 0.011 0.001 PHE A 159 TRP 0.034 0.001 TRP K 35 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00483 (20073) covalent geometry : angle 0.64081 (27234) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.85141 ( 84) hydrogen bonds : bond 0.03699 ( 567) hydrogen bonds : angle 4.96589 ( 1512) link_ALPHA1-2 : bond 0.00090 ( 3) link_ALPHA1-2 : angle 1.74267 ( 9) link_ALPHA1-3 : bond 0.01278 ( 9) link_ALPHA1-3 : angle 3.48890 ( 27) link_ALPHA1-6 : bond 0.00965 ( 6) link_ALPHA1-6 : angle 0.98044 ( 18) link_BETA1-2 : bond 0.00461 ( 3) link_BETA1-2 : angle 1.89664 ( 9) link_BETA1-4 : bond 0.00388 ( 27) link_BETA1-4 : angle 2.18645 ( 81) link_NAG-ASN : bond 0.00289 ( 42) link_NAG-ASN : angle 2.01536 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 352 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7564 (m-30) cc_final: 0.7268 (m-30) REVERT: A 296 CYS cc_start: 0.5480 (m) cc_final: 0.5250 (m) REVERT: C 296 CYS cc_start: 0.5715 (m) cc_final: 0.5494 (m) REVERT: C 475 MET cc_start: 0.8704 (tpp) cc_final: 0.8370 (tpp) REVERT: D 574 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8114 (ttmt) REVERT: D 646 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8909 (mm) REVERT: D 652 GLN cc_start: 0.8636 (tt0) cc_final: 0.8278 (tt0) REVERT: D 653 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: D 656 ASN cc_start: 0.8918 (m-40) cc_final: 0.8504 (m110) REVERT: D 657 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7965 (tp30) REVERT: E 107 ASP cc_start: 0.7429 (m-30) cc_final: 0.7077 (m-30) REVERT: E 153 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: F 605 CYS cc_start: 0.7605 (m) cc_final: 0.7173 (m) REVERT: F 647 GLU cc_start: 0.8133 (tt0) cc_final: 0.7930 (tt0) REVERT: F 656 ASN cc_start: 0.8725 (m-40) cc_final: 0.8103 (m110) REVERT: H 18 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6111 (mm) REVERT: H 38 ARG cc_start: 0.6602 (ttp80) cc_final: 0.6287 (tmm160) REVERT: J 29 LEU cc_start: 0.8640 (mm) cc_final: 0.8420 (mt) REVERT: J 67 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6145 (mm) REVERT: L 86 TYR cc_start: 0.7843 (m-80) cc_final: 0.7551 (m-80) REVERT: L 92 ASP cc_start: 0.8420 (t0) cc_final: 0.8205 (t70) REVERT: M 18 LEU cc_start: 0.5690 (OUTLIER) cc_final: 0.5461 (mm) REVERT: M 67 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6472 (mm) REVERT: N 3 GLN cc_start: 0.8681 (mp10) cc_final: 0.8324 (mp10) outliers start: 78 outliers final: 59 residues processed: 405 average time/residue: 0.1467 time to fit residues: 91.2106 Evaluate side-chains 404 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 190 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 209 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104965 restraints weight = 30966.512| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.58 r_work: 0.3129 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20205 Z= 0.163 Angle : 0.663 8.394 27588 Z= 0.319 Chirality : 0.046 0.233 3330 Planarity : 0.004 0.054 3327 Dihedral : 7.506 60.852 4344 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.11 % Allowed : 17.67 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2295 helix: 0.86 (0.27), residues: 429 sheet: -0.73 (0.20), residues: 708 loop : -1.02 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 38 TYR 0.026 0.002 TYR F 638 PHE 0.011 0.001 PHE L 89 TRP 0.034 0.001 TRP K 35 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00389 (20073) covalent geometry : angle 0.62488 (27234) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.97376 ( 84) hydrogen bonds : bond 0.03530 ( 567) hydrogen bonds : angle 4.87475 ( 1512) link_ALPHA1-2 : bond 0.00056 ( 3) link_ALPHA1-2 : angle 1.73854 ( 9) link_ALPHA1-3 : bond 0.01358 ( 9) link_ALPHA1-3 : angle 3.27219 ( 27) link_ALPHA1-6 : bond 0.00981 ( 6) link_ALPHA1-6 : angle 0.98320 ( 18) link_BETA1-2 : bond 0.00411 ( 3) link_BETA1-2 : angle 1.89759 ( 9) link_BETA1-4 : bond 0.00379 ( 27) link_BETA1-4 : angle 2.08338 ( 81) link_NAG-ASN : bond 0.00230 ( 42) link_NAG-ASN : angle 1.88319 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 344 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7516 (m-30) cc_final: 0.7188 (m-30) REVERT: A 173 TYR cc_start: 0.8791 (p90) cc_final: 0.8577 (p90) REVERT: D 657 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7968 (tp30) REVERT: E 103 GLN cc_start: 0.8128 (tt0) cc_final: 0.7565 (tt0) REVERT: E 107 ASP cc_start: 0.7383 (m-30) cc_final: 0.7032 (m-30) REVERT: E 116 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7457 (mp) REVERT: E 153 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: F 605 CYS cc_start: 0.7559 (m) cc_final: 0.7157 (m) REVERT: F 617 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7833 (mtt180) REVERT: F 653 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: H 38 ARG cc_start: 0.6612 (ttp80) cc_final: 0.6319 (tmm160) REVERT: J 67 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6076 (mm) REVERT: L 79 GLN cc_start: 0.8565 (pp30) cc_final: 0.7646 (mt0) REVERT: M 67 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6455 (mm) REVERT: M 107 THR cc_start: 0.6253 (OUTLIER) cc_final: 0.6001 (p) REVERT: N 3 GLN cc_start: 0.8701 (mp10) cc_final: 0.8320 (mp10) REVERT: N 27 GLN cc_start: 0.7516 (mp10) cc_final: 0.7245 (mp10) REVERT: N 86 TYR cc_start: 0.7718 (m-80) cc_final: 0.7276 (m-80) outliers start: 84 outliers final: 55 residues processed: 401 average time/residue: 0.1539 time to fit residues: 94.0047 Evaluate side-chains 391 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 330 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 225 optimal weight: 0.0470 chunk 228 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106390 restraints weight = 30848.584| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.68 r_work: 0.3145 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20205 Z= 0.146 Angle : 0.657 13.046 27588 Z= 0.313 Chirality : 0.046 0.289 3330 Planarity : 0.004 0.055 3327 Dihedral : 7.139 59.905 4344 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.03 % Allowed : 18.94 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2295 helix: 1.15 (0.28), residues: 411 sheet: -0.57 (0.20), residues: 729 loop : -0.99 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.030 0.002 TYR F 638 PHE 0.011 0.001 PHE K 89 TRP 0.038 0.001 TRP K 35 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00345 (20073) covalent geometry : angle 0.62311 (27234) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.76992 ( 84) hydrogen bonds : bond 0.03391 ( 567) hydrogen bonds : angle 4.76827 ( 1512) link_ALPHA1-2 : bond 0.00067 ( 3) link_ALPHA1-2 : angle 1.74689 ( 9) link_ALPHA1-3 : bond 0.01387 ( 9) link_ALPHA1-3 : angle 3.08212 ( 27) link_ALPHA1-6 : bond 0.00909 ( 6) link_ALPHA1-6 : angle 1.04972 ( 18) link_BETA1-2 : bond 0.00424 ( 3) link_BETA1-2 : angle 1.86515 ( 9) link_BETA1-4 : bond 0.00388 ( 27) link_BETA1-4 : angle 2.01170 ( 81) link_NAG-ASN : bond 0.00233 ( 42) link_NAG-ASN : angle 1.80426 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8067 (tt0) cc_final: 0.7424 (tt0) REVERT: A 107 ASP cc_start: 0.7441 (m-30) cc_final: 0.7145 (m-30) REVERT: B 542 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7956 (mtm-85) REVERT: D 634 GLU cc_start: 0.8377 (tt0) cc_final: 0.8140 (mt-10) REVERT: D 647 GLU cc_start: 0.7738 (tt0) cc_final: 0.7053 (tt0) REVERT: D 656 ASN cc_start: 0.8934 (m-40) cc_final: 0.8520 (m110) REVERT: E 103 GLN cc_start: 0.8142 (tt0) cc_final: 0.7558 (tt0) REVERT: E 107 ASP cc_start: 0.7349 (m-30) cc_final: 0.7007 (m-30) REVERT: E 116 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7527 (mp) REVERT: E 153 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: F 530 MET cc_start: 0.8781 (mmm) cc_final: 0.8237 (mtp) REVERT: F 542 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8373 (mtm-85) REVERT: F 605 CYS cc_start: 0.7533 (m) cc_final: 0.7116 (m) REVERT: F 653 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: H 38 ARG cc_start: 0.6601 (ttp80) cc_final: 0.6356 (tmm160) REVERT: H 111 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6396 (p) REVERT: J 38 ARG cc_start: 0.6730 (ttp80) cc_final: 0.6229 (tmm160) REVERT: J 67 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6015 (mm) REVERT: M 67 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6439 (mm) REVERT: M 100 MET cc_start: 0.8094 (mtt) cc_final: 0.7890 (mtt) REVERT: M 107 THR cc_start: 0.6166 (OUTLIER) cc_final: 0.5943 (p) REVERT: N 3 GLN cc_start: 0.8699 (mp10) cc_final: 0.8319 (mp10) REVERT: N 79 GLN cc_start: 0.8395 (mm110) cc_final: 0.8021 (mp10) REVERT: N 86 TYR cc_start: 0.7696 (m-80) cc_final: 0.7319 (m-80) outliers start: 62 outliers final: 44 residues processed: 376 average time/residue: 0.1635 time to fit residues: 93.2926 Evaluate side-chains 381 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 208 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN J 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103480 restraints weight = 31300.178| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.70 r_work: 0.3091 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20205 Z= 0.218 Angle : 0.708 11.688 27588 Z= 0.338 Chirality : 0.047 0.310 3330 Planarity : 0.005 0.055 3327 Dihedral : 7.350 58.659 4344 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.79 % Allowed : 19.48 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.18), residues: 2295 helix: 1.02 (0.28), residues: 411 sheet: -0.64 (0.20), residues: 708 loop : -1.06 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 24 TYR 0.034 0.002 TYR F 638 PHE 0.013 0.001 PHE L 89 TRP 0.037 0.001 TRP K 35 HIS 0.007 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00526 (20073) covalent geometry : angle 0.67146 (27234) SS BOND : bond 0.00453 ( 42) SS BOND : angle 2.07915 ( 84) hydrogen bonds : bond 0.03650 ( 567) hydrogen bonds : angle 4.86944 ( 1512) link_ALPHA1-2 : bond 0.00115 ( 3) link_ALPHA1-2 : angle 1.77571 ( 9) link_ALPHA1-3 : bond 0.01282 ( 9) link_ALPHA1-3 : angle 2.92301 ( 27) link_ALPHA1-6 : bond 0.00844 ( 6) link_ALPHA1-6 : angle 1.04031 ( 18) link_BETA1-2 : bond 0.00459 ( 3) link_BETA1-2 : angle 1.87483 ( 9) link_BETA1-4 : bond 0.00383 ( 27) link_BETA1-4 : angle 2.11417 ( 81) link_NAG-ASN : bond 0.00337 ( 42) link_NAG-ASN : angle 2.05582 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8126 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 107 ASP cc_start: 0.7482 (m-30) cc_final: 0.6968 (m-30) REVERT: D 647 GLU cc_start: 0.7881 (tt0) cc_final: 0.7144 (tt0) REVERT: E 99 ASN cc_start: 0.8766 (t0) cc_final: 0.8376 (t0) REVERT: E 103 GLN cc_start: 0.8196 (tt0) cc_final: 0.7574 (tt0) REVERT: E 107 ASP cc_start: 0.7425 (m-30) cc_final: 0.7052 (m-30) REVERT: E 116 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7548 (mp) REVERT: E 153 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: F 530 MET cc_start: 0.8822 (mmm) cc_final: 0.8226 (mtp) REVERT: F 542 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8372 (mtm-85) REVERT: F 605 CYS cc_start: 0.7598 (m) cc_final: 0.7218 (m) REVERT: F 653 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: H 38 ARG cc_start: 0.6628 (ttp80) cc_final: 0.6414 (tmm160) REVERT: H 111 VAL cc_start: 0.6788 (OUTLIER) cc_final: 0.6346 (p) REVERT: J 38 ARG cc_start: 0.6865 (ttp80) cc_final: 0.6445 (tmm160) REVERT: J 67 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6015 (mm) REVERT: M 67 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6461 (mm) REVERT: M 100 MET cc_start: 0.8198 (mtt) cc_final: 0.7929 (mtt) REVERT: M 107 THR cc_start: 0.6204 (OUTLIER) cc_final: 0.5977 (p) REVERT: N 3 GLN cc_start: 0.8688 (mp10) cc_final: 0.8303 (mp10) REVERT: N 79 GLN cc_start: 0.8386 (mm110) cc_final: 0.7956 (mp10) REVERT: N 86 TYR cc_start: 0.7768 (m-80) cc_final: 0.7460 (m-80) outliers start: 57 outliers final: 46 residues processed: 375 average time/residue: 0.1576 time to fit residues: 89.6711 Evaluate side-chains 381 residues out of total 2061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 189 optimal weight: 7.9990 chunk 146 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105115 restraints weight = 31081.498| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.66 r_work: 0.3128 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20205 Z= 0.150 Angle : 0.669 11.892 27588 Z= 0.319 Chirality : 0.046 0.302 3330 Planarity : 0.004 0.059 3327 Dihedral : 6.953 58.948 4344 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.64 % Allowed : 19.68 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2295 helix: 1.19 (0.28), residues: 408 sheet: -0.52 (0.20), residues: 705 loop : -1.02 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 24 TYR 0.035 0.002 TYR F 638 PHE 0.010 0.001 PHE L 89 TRP 0.038 0.001 TRP K 35 HIS 0.006 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00354 (20073) covalent geometry : angle 0.63536 (27234) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.93645 ( 84) hydrogen bonds : bond 0.03373 ( 567) hydrogen bonds : angle 4.78573 ( 1512) link_ALPHA1-2 : bond 0.00069 ( 3) link_ALPHA1-2 : angle 1.77320 ( 9) link_ALPHA1-3 : bond 0.01389 ( 9) link_ALPHA1-3 : angle 2.85382 ( 27) link_ALPHA1-6 : bond 0.00871 ( 6) link_ALPHA1-6 : angle 1.08265 ( 18) link_BETA1-2 : bond 0.00415 ( 3) link_BETA1-2 : angle 1.84380 ( 9) link_BETA1-4 : bond 0.00379 ( 27) link_BETA1-4 : angle 1.96253 ( 81) link_NAG-ASN : bond 0.00235 ( 42) link_NAG-ASN : angle 1.80082 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.12 seconds wall clock time: 73 minutes 57.62 seconds (4437.62 seconds total)