Starting phenix.real_space_refine on Thu Feb 5 23:32:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o2s_70020/02_2026/9o2s_70020.map" } resolution = 3.2 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= 0.022 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 12975 2.51 5 N 3462 2.21 5 O 4117 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: 20686 Number of models: 1 Model: "" Number of chains: 34 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: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 5 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: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1645 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1645 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 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: 4.22, per 1000 atoms: 0.20 Number of scatterers: 20686 At special positions: 0 Unit cell: (114.816, 178.048, 169.728, 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 4117 8.00 N 3462 7.00 C 12975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 208 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.05 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 Q 7 " - " MAN Q 8 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA Q 3 " - " MAN Q 7 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " " MAN Q 4 " - " NAG Q 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG Q 5 " - " GAL Q 6 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 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 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 386 " " NAG E 606 " - " ASN E 133 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 301 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN E 160 " " NAG X 1 " - " ASN E 197 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 363 " " NAG b 1 " - " ASN E 448 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 839.9 milliseconds 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 18.8% alpha, 26.6% 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: 3.759A 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: 3.773A 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: 3.543A 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: 3.514A 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: 3.542A 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: 3.743A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.385A 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: 4.002A 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: 3.569A 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 98 through 114 removed outlier: 3.934A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.602A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.664A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (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: 3.528A 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 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 213 through 216 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 213 through 216 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.860A 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: 8.090A 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: 4.001A 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: 5.003A 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: 7.799A 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: 7.986A 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: 3.668A 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: 6.707A 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: 6.687A 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: 5.114A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.118A 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: 4.120A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.683A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.436A pdb=" N CYS E 201 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.595A pdb=" N SER E 158 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC1, 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 302 removed outlier: 7.748A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 334 current: chain 'E' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC4, 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: 6.605A 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=AC5, first strand: chain 'H' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 147 current: chain 'H' and resid 185 through 194 Processing sheet with id=AC6, first strand: chain 'H' and resid 153 through 157 Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.712A 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: 3.757A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 137 through 147 current: chain 'J' and resid 185 through 194 Processing sheet with id=AD1, first strand: chain 'J' and resid 153 through 157 Processing sheet with id=AD2, 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=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.587A 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=AD4, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.620A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AD6, 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=AD7, 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=AD8, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.621A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 153 through 154 617 hydrogen bonds defined for protein. 1653 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: 3.63 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 8510 1.42 - 1.63: 12410 1.63 - 1.84: 172 1.84 - 2.05: 5 2.05 - 2.26: 1 Bond restraints: 21098 Sorted by residual: bond pdb=" C SER J 112 " pdb=" N ALA J 114 " ideal model delta sigma weight residual 1.329 2.260 -0.931 1.40e-02 5.10e+03 4.42e+03 bond pdb=" C SER H 112 " pdb=" N ALA H 114 " ideal model delta sigma weight residual 1.329 1.962 -0.633 1.40e-02 5.10e+03 2.04e+03 bond pdb=" CA SER H 32 " pdb=" CB SER H 32 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.49e-02 4.50e+03 1.10e+01 bond pdb=" CA SER J 32 " pdb=" CB SER J 32 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.49e-02 4.50e+03 1.09e+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 7.21e+00 ... (remaining 21093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 28652 10.07 - 20.14: 7 20.14 - 30.21: 1 30.21 - 40.28: 1 40.28 - 50.36: 2 Bond angle restraints: 28663 Sorted by residual: angle pdb=" O SER H 112 " pdb=" C SER H 112 " pdb=" N ALA H 114 " ideal model delta sigma weight residual 122.59 72.23 50.36 1.33e+00 5.65e-01 1.43e+03 angle pdb=" O SER J 112 " pdb=" C SER J 112 " pdb=" N ALA J 114 " ideal model delta sigma weight residual 122.59 77.86 44.73 1.33e+00 5.65e-01 1.13e+03 angle pdb=" C SER J 112 " pdb=" N ALA J 114 " pdb=" CA ALA J 114 " ideal model delta sigma weight residual 121.70 160.17 -38.47 1.80e+00 3.09e-01 4.57e+02 angle pdb=" CA SER H 112 " pdb=" C SER H 112 " pdb=" N ALA H 114 " ideal model delta sigma weight residual 116.84 144.70 -27.86 1.71e+00 3.42e-01 2.65e+02 angle pdb=" C SER H 112 " pdb=" N ALA H 114 " pdb=" CA ALA H 114 " ideal model delta sigma weight residual 121.70 134.89 -13.19 1.80e+00 3.09e-01 5.37e+01 ... (remaining 28658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12915 22.64 - 45.28: 572 45.28 - 67.92: 122 67.92 - 90.55: 51 90.55 - 113.19: 28 Dihedral angle restraints: 13688 sinusoidal: 6421 harmonic: 7267 Sorted by residual: 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 -4.12 -81.88 1 1.00e+01 1.00e-02 8.24e+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 -5.65 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -5.68 -80.32 1 1.00e+01 1.00e-02 7.99e+01 ... (remaining 13685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3429 0.164 - 0.329: 53 0.329 - 0.493: 8 0.493 - 0.658: 0 0.658 - 0.822: 4 Chirality restraints: 3494 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 1.72 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 MAN Q 4 " pdb=" O6 BMA Q 3 " pdb=" C2 MAN Q 4 " pdb=" O5 MAN Q 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 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.77e+02 ... (remaining 3491 not shown) Planarity restraints: 3574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 112 " 0.174 2.00e-02 2.50e+03 2.43e-01 5.91e+02 pdb=" C SER J 112 " -0.412 2.00e-02 2.50e+03 pdb=" O SER J 112 " 0.181 2.00e-02 2.50e+03 pdb=" N ALA J 114 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.234 2.00e-02 2.50e+03 1.96e-01 4.81e+02 pdb=" C7 NAG E 602 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 112 " -0.131 2.00e-02 2.50e+03 1.63e-01 2.66e+02 pdb=" C SER H 112 " 0.280 2.00e-02 2.50e+03 pdb=" O SER H 112 " -0.069 2.00e-02 2.50e+03 pdb=" N ALA H 114 " -0.080 2.00e-02 2.50e+03 ... (remaining 3571 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 129 2.54 - 3.13: 15353 3.13 - 3.72: 30670 3.72 - 4.31: 47330 4.31 - 4.90: 78284 Nonbonded interactions: 171766 Sorted by model distance: nonbonded pdb=" O ILE C 491 " pdb=" NH2 ARG D 585 " model vdw 1.951 3.120 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR D 606 " model vdw 1.982 3.040 nonbonded pdb=" OG SER D 528 " pdb=" O7 NAG C 601 " model vdw 2.031 3.040 nonbonded pdb=" OG SER B 528 " pdb=" O7 NAG A 601 " model vdw 2.149 3.040 nonbonded pdb=" O THR K 107 " pdb=" CZ TYR K 140 " model vdw 2.183 3.260 ... (remaining 171761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 606) selection = (chain 'C' and resid 34 through 606) selection = (chain 'E' and (resid 34 through 137 or resid 148 through 606)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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: 5.250 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.350 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 : 0.011 0.931 21221 Z= 0.658 Angle : 1.024 50.356 28989 Z= 0.555 Chirality : 0.065 0.822 3494 Planarity : 0.008 0.243 3533 Dihedral : 14.530 113.193 8855 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 0.23 % Allowed : 1.37 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.04 % 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: -1.18 (0.17), residues: 2453 helix: -1.53 (0.23), residues: 450 sheet: -0.24 (0.19), residues: 778 loop : -0.74 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 444 TYR 0.055 0.003 TYR L 140 PHE 0.026 0.002 PHE J 100K TRP 0.014 0.001 TRP H 34 HIS 0.006 0.001 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00992 (21098) covalent geometry : angle 0.95482 (28663) SS BOND : bond 0.08730 ( 43) SS BOND : angle 3.16697 ( 86) hydrogen bonds : bond 0.22879 ( 617) hydrogen bonds : angle 8.65946 ( 1653) link_ALPHA1-2 : bond 0.00604 ( 2) link_ALPHA1-2 : angle 3.40829 ( 6) link_ALPHA1-3 : bond 0.02059 ( 6) link_ALPHA1-3 : angle 6.52878 ( 18) link_ALPHA1-6 : bond 0.00352 ( 4) link_ALPHA1-6 : angle 3.58760 ( 12) link_BETA1-2 : bond 0.00254 ( 2) link_BETA1-2 : angle 3.53533 ( 6) link_BETA1-4 : bond 0.01545 ( 25) link_BETA1-4 : angle 4.07477 ( 75) link_NAG-ASN : bond 0.00849 ( 41) link_NAG-ASN : angle 2.94073 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4906 Ramachandran restraints generated. 2453 Oldfield, 0 Emsley, 2453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 502 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9226 (m) cc_final: 0.8890 (p) REVERT: A 189 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7105 (mmmt) REVERT: B 632 ASP cc_start: 0.8270 (t70) cc_final: 0.7960 (t70) REVERT: B 657 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7744 (tp30) REVERT: B 660 LEU cc_start: 0.8535 (tt) cc_final: 0.8237 (tp) REVERT: C 46 LYS cc_start: 0.8363 (mmpt) cc_final: 0.8111 (mmtm) REVERT: C 189 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6788 (mmtp) REVERT: D 632 ASP cc_start: 0.8578 (t70) cc_final: 0.8300 (t0) REVERT: E 217 TYR cc_start: 0.7243 (m-80) cc_final: 0.6934 (m-80) REVERT: E 325 ASP cc_start: 0.7123 (p0) cc_final: 0.6830 (p0) REVERT: E 432 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7600 (mp10) REVERT: J 5 GLN cc_start: 0.6842 (mt0) cc_final: 0.6613 (mt0) REVERT: J 36 TRP cc_start: 0.8250 (m100) cc_final: 0.8034 (m100) REVERT: K 93 SER cc_start: 0.6872 (m) cc_final: 0.6359 (p) REVERT: K 100 GLN cc_start: 0.7476 (mp10) cc_final: 0.6919 (mp10) REVERT: L 3 GLN cc_start: 0.7533 (mp10) cc_final: 0.7082 (mp10) REVERT: L 66 ARG cc_start: 0.6642 (tpt90) cc_final: 0.6380 (tpt170) REVERT: L 76 LYS cc_start: 0.7581 (mptt) cc_final: 0.6932 (mmtm) REVERT: L 79 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7870 (mm-40) outliers start: 5 outliers final: 1 residues processed: 506 average time/residue: 0.1630 time to fit residues: 121.1159 Evaluate side-chains 284 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 54 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 195 ASN A 356 ASN A 411 ASN B 652 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 356 ASN C 411 ASN D 540 GLN D 625 ASN E 94 ASN E 137 ASN F 630 GLN J 57 HIS K 155 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 155 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.168236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118379 restraints weight = 29590.077| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.65 r_work: 0.3285 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21221 Z= 0.151 Angle : 0.716 18.329 28989 Z= 0.352 Chirality : 0.047 0.330 3494 Planarity : 0.005 0.054 3533 Dihedral : 9.371 78.430 4311 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 8.28 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.50 (0.17), residues: 2455 helix: -0.32 (0.25), residues: 453 sheet: 0.10 (0.19), residues: 779 loop : -0.52 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 542 TYR 0.017 0.002 TYR E 191 PHE 0.017 0.001 PHE J 100 TRP 0.014 0.001 TRP E 69 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00347 (21098) covalent geometry : angle 0.67213 (28663) SS BOND : bond 0.00446 ( 43) SS BOND : angle 2.58626 ( 86) hydrogen bonds : bond 0.04515 ( 617) hydrogen bonds : angle 5.83850 ( 1653) link_ALPHA1-2 : bond 0.00045 ( 2) link_ALPHA1-2 : angle 1.65786 ( 6) link_ALPHA1-3 : bond 0.00974 ( 6) link_ALPHA1-3 : angle 4.64303 ( 18) link_ALPHA1-6 : bond 0.00842 ( 4) link_ALPHA1-6 : angle 1.82204 ( 12) link_BETA1-2 : bond 0.00378 ( 2) link_BETA1-2 : angle 1.77743 ( 6) link_BETA1-4 : bond 0.00661 ( 25) link_BETA1-4 : angle 2.37683 ( 75) link_NAG-ASN : bond 0.00289 ( 41) link_NAG-ASN : angle 1.92476 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9294 (m) cc_final: 0.8901 (p) REVERT: A 54 CYS cc_start: 0.7178 (t) cc_final: 0.6960 (t) REVERT: A 189 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6502 (mmmt) REVERT: B 542 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8067 (mtm110) REVERT: B 632 ASP cc_start: 0.8749 (t70) cc_final: 0.8280 (t0) REVERT: B 660 LEU cc_start: 0.8189 (tt) cc_final: 0.7959 (tp) REVERT: C 46 LYS cc_start: 0.8670 (mmpt) cc_final: 0.8455 (mmtm) REVERT: C 411 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.5850 (t0) REVERT: D 617 ARG cc_start: 0.8482 (mtp180) cc_final: 0.7886 (mtp180) REVERT: D 632 ASP cc_start: 0.8793 (t70) cc_final: 0.8360 (t0) REVERT: E 151 ARG cc_start: 0.7805 (ttt90) cc_final: 0.7597 (tpp80) REVERT: E 217 TYR cc_start: 0.7811 (m-80) cc_final: 0.7417 (m-80) REVERT: E 370 GLU cc_start: 0.7652 (mp0) cc_final: 0.7069 (mt-10) REVERT: E 432 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7361 (mp10) REVERT: F 654 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7282 (mt-10) REVERT: F 655 LYS cc_start: 0.7958 (pttt) cc_final: 0.7583 (mtpt) REVERT: H 91 TYR cc_start: 0.8029 (m-80) cc_final: 0.7800 (m-80) REVERT: J 36 TRP cc_start: 0.8231 (m100) cc_final: 0.8004 (m100) REVERT: K 81 GLU cc_start: 0.7533 (pm20) cc_final: 0.7216 (pm20) REVERT: K 93 SER cc_start: 0.7699 (m) cc_final: 0.7292 (p) REVERT: K 100 GLN cc_start: 0.8195 (mp10) cc_final: 0.7322 (mp10) REVERT: K 207 LYS cc_start: 0.2761 (mtpt) cc_final: 0.1505 (pptt) REVERT: L 3 GLN cc_start: 0.7930 (mp10) cc_final: 0.7611 (mp10) REVERT: L 6 GLN cc_start: 0.6377 (tp-100) cc_final: 0.5902 (tp40) REVERT: L 66 ARG cc_start: 0.7188 (tpt90) cc_final: 0.6750 (tpt170) REVERT: L 74 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8064 (ttpp) REVERT: L 103 LYS cc_start: 0.8096 (mtmt) cc_final: 0.6686 (ttpp) REVERT: L 199 GLN cc_start: 0.7132 (tt0) cc_final: 0.6153 (mp10) outliers start: 37 outliers final: 22 residues processed: 349 average time/residue: 0.1512 time to fit residues: 80.1855 Evaluate side-chains 287 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain H residue 7 TRP Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN A 425 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 428 GLN E 85 HIS E 293 GLN H 25 HIS J 6 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110627 restraints weight = 29771.445| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.20 r_work: 0.3187 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 21221 Z= 0.267 Angle : 0.767 17.315 28989 Z= 0.376 Chirality : 0.049 0.292 3494 Planarity : 0.005 0.067 3533 Dihedral : 8.992 80.502 4311 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.47 % Allowed : 11.34 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.58 (0.17), residues: 2455 helix: -0.18 (0.25), residues: 451 sheet: 0.04 (0.20), residues: 750 loop : -0.65 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 327 TYR 0.019 0.002 TYR E 191 PHE 0.019 0.002 PHE J 122 TRP 0.029 0.002 TRP K 35 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00646 (21098) covalent geometry : angle 0.72440 (28663) SS BOND : bond 0.00929 ( 43) SS BOND : angle 2.73548 ( 86) hydrogen bonds : bond 0.04531 ( 617) hydrogen bonds : angle 5.56171 ( 1653) link_ALPHA1-2 : bond 0.00438 ( 2) link_ALPHA1-2 : angle 2.12022 ( 6) link_ALPHA1-3 : bond 0.00799 ( 6) link_ALPHA1-3 : angle 4.24459 ( 18) link_ALPHA1-6 : bond 0.00787 ( 4) link_ALPHA1-6 : angle 1.37679 ( 12) link_BETA1-2 : bond 0.00120 ( 2) link_BETA1-2 : angle 1.96721 ( 6) link_BETA1-4 : bond 0.00545 ( 25) link_BETA1-4 : angle 2.35781 ( 75) link_NAG-ASN : bond 0.00467 ( 41) link_NAG-ASN : angle 2.15442 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9367 (m) cc_final: 0.8962 (p) REVERT: A 189 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6599 (mmmt) REVERT: B 632 ASP cc_start: 0.8911 (t70) cc_final: 0.8425 (t0) REVERT: B 647 GLU cc_start: 0.8282 (tt0) cc_final: 0.8050 (tt0) REVERT: B 657 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7791 (tp30) REVERT: B 660 LEU cc_start: 0.8255 (tt) cc_final: 0.7921 (tp) REVERT: C 46 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8537 (mmtm) REVERT: C 51 THR cc_start: 0.9493 (m) cc_final: 0.9249 (t) REVERT: D 542 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8000 (ttp-170) REVERT: D 632 ASP cc_start: 0.8905 (t70) cc_final: 0.8562 (t0) REVERT: D 656 ASN cc_start: 0.8089 (t0) cc_final: 0.7878 (t0) REVERT: E 35 TRP cc_start: 0.8367 (m-90) cc_final: 0.7936 (m-90) REVERT: E 69 TRP cc_start: 0.7210 (m-90) cc_final: 0.7001 (m-90) REVERT: E 97 LYS cc_start: 0.8626 (mppt) cc_final: 0.8311 (mtmm) REVERT: E 207 LYS cc_start: 0.8425 (mmtp) cc_final: 0.7964 (ptmt) REVERT: E 370 GLU cc_start: 0.7941 (mp0) cc_final: 0.7491 (mt-10) REVERT: E 475 MET cc_start: 0.8583 (mmm) cc_final: 0.8290 (tpp) REVERT: F 655 LYS cc_start: 0.7956 (pttt) cc_final: 0.7587 (mtmt) REVERT: H 184 LEU cc_start: 0.5856 (mm) cc_final: 0.5135 (tp) REVERT: H 185 TYR cc_start: 0.7175 (m-80) cc_final: 0.6870 (m-80) REVERT: J 36 TRP cc_start: 0.8232 (m100) cc_final: 0.7978 (m100) REVERT: K 93 SER cc_start: 0.7814 (m) cc_final: 0.7362 (p) REVERT: K 207 LYS cc_start: 0.3056 (mtpt) cc_final: 0.1775 (pptt) REVERT: L 3 GLN cc_start: 0.7846 (mp10) cc_final: 0.7516 (mp10) REVERT: L 66 ARG cc_start: 0.7308 (tpt90) cc_final: 0.6780 (tpt170) REVERT: L 100 GLN cc_start: 0.8205 (mm-40) cc_final: 0.6947 (mp10) REVERT: L 140 TYR cc_start: 0.6108 (t80) cc_final: 0.5798 (t80) outliers start: 54 outliers final: 37 residues processed: 329 average time/residue: 0.1512 time to fit residues: 75.6471 Evaluate side-chains 291 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 7 TRP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 221 optimal weight: 10.0000 chunk 132 optimal weight: 0.0070 chunk 113 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 156 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN E 377 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.164432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114413 restraints weight = 29583.147| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.33 r_work: 0.3245 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21221 Z= 0.121 Angle : 0.649 15.243 28989 Z= 0.316 Chirality : 0.045 0.296 3494 Planarity : 0.004 0.053 3533 Dihedral : 7.928 68.789 4309 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.88 % Allowed : 12.95 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2455 helix: 0.30 (0.26), residues: 451 sheet: -0.02 (0.19), residues: 773 loop : -0.56 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100J TYR 0.019 0.001 TYR H 91 PHE 0.013 0.001 PHE J 148 TRP 0.015 0.001 TRP K 35 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00273 (21098) covalent geometry : angle 0.60704 (28663) SS BOND : bond 0.00712 ( 43) SS BOND : angle 2.41174 ( 86) hydrogen bonds : bond 0.03581 ( 617) hydrogen bonds : angle 5.17092 ( 1653) link_ALPHA1-2 : bond 0.00116 ( 2) link_ALPHA1-2 : angle 1.77489 ( 6) link_ALPHA1-3 : bond 0.00983 ( 6) link_ALPHA1-3 : angle 4.42764 ( 18) link_ALPHA1-6 : bond 0.00994 ( 4) link_ALPHA1-6 : angle 1.18158 ( 12) link_BETA1-2 : bond 0.00284 ( 2) link_BETA1-2 : angle 2.05445 ( 6) link_BETA1-4 : bond 0.00565 ( 25) link_BETA1-4 : angle 2.12520 ( 75) link_NAG-ASN : bond 0.00323 ( 41) link_NAG-ASN : angle 1.76075 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9326 (m) cc_final: 0.8912 (p) REVERT: A 189 LYS cc_start: 0.7127 (mmtt) cc_final: 0.6481 (mmmt) REVERT: B 632 ASP cc_start: 0.8880 (t70) cc_final: 0.8497 (t70) REVERT: B 657 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7758 (tp30) REVERT: B 660 LEU cc_start: 0.8212 (tt) cc_final: 0.7899 (tp) REVERT: C 46 LYS cc_start: 0.8808 (mmpt) cc_final: 0.8563 (mmtm) REVERT: D 632 ASP cc_start: 0.8829 (t70) cc_final: 0.8326 (t0) REVERT: D 656 ASN cc_start: 0.8108 (t0) cc_final: 0.7864 (t0) REVERT: E 35 TRP cc_start: 0.8205 (m-90) cc_final: 0.7892 (m100) REVERT: E 97 LYS cc_start: 0.8575 (mppt) cc_final: 0.8248 (mtmm) REVERT: E 207 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7813 (ptmt) REVERT: E 370 GLU cc_start: 0.7854 (mp0) cc_final: 0.7398 (mt-10) REVERT: E 432 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: E 475 MET cc_start: 0.8491 (mmm) cc_final: 0.8236 (tpp) REVERT: F 654 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7547 (mt-10) REVERT: F 655 LYS cc_start: 0.7921 (pttt) cc_final: 0.7553 (mtmt) REVERT: H 83 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.6023 (p) REVERT: H 185 TYR cc_start: 0.7200 (m-80) cc_final: 0.6857 (m-80) REVERT: J 52 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: K 81 GLU cc_start: 0.7460 (pm20) cc_final: 0.7077 (pm20) REVERT: K 93 SER cc_start: 0.7879 (m) cc_final: 0.7437 (p) REVERT: L 3 GLN cc_start: 0.7783 (mp10) cc_final: 0.7466 (mp10) REVERT: L 66 ARG cc_start: 0.7259 (tpt90) cc_final: 0.6741 (tpt170) REVERT: L 76 LYS cc_start: 0.7824 (mppt) cc_final: 0.7460 (mptt) REVERT: L 81 GLU cc_start: 0.7611 (pm20) cc_final: 0.7286 (pm20) REVERT: L 100 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7011 (mp10) REVERT: L 103 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7533 (mtmm) outliers start: 41 outliers final: 23 residues processed: 312 average time/residue: 0.1448 time to fit residues: 69.1101 Evaluate side-chains 278 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 239 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 0.0170 chunk 118 optimal weight: 3.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN C 188 ASN C 293 GLN C 300 ASN C 356 ASN F 630 GLN K 166 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.162813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112601 restraints weight = 29479.048| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.40 r_work: 0.3202 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21221 Z= 0.166 Angle : 0.663 13.827 28989 Z= 0.322 Chirality : 0.046 0.293 3494 Planarity : 0.004 0.055 3533 Dihedral : 7.623 68.424 4309 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.38 % Allowed : 13.13 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.30 (0.17), residues: 2455 helix: 0.38 (0.26), residues: 451 sheet: 0.14 (0.20), residues: 755 loop : -0.56 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 504 TYR 0.015 0.001 TYR B 638 PHE 0.013 0.001 PHE J 148 TRP 0.011 0.001 TRP A 96 HIS 0.008 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00397 (21098) covalent geometry : angle 0.61813 (28663) SS BOND : bond 0.00644 ( 43) SS BOND : angle 2.62809 ( 86) hydrogen bonds : bond 0.03584 ( 617) hydrogen bonds : angle 5.08742 ( 1653) link_ALPHA1-2 : bond 0.00228 ( 2) link_ALPHA1-2 : angle 1.90073 ( 6) link_ALPHA1-3 : bond 0.00908 ( 6) link_ALPHA1-3 : angle 4.33488 ( 18) link_ALPHA1-6 : bond 0.00820 ( 4) link_ALPHA1-6 : angle 1.17728 ( 12) link_BETA1-2 : bond 0.00234 ( 2) link_BETA1-2 : angle 1.95573 ( 6) link_BETA1-4 : bond 0.00539 ( 25) link_BETA1-4 : angle 2.15536 ( 75) link_NAG-ASN : bond 0.00334 ( 41) link_NAG-ASN : angle 1.87969 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9344 (m) cc_final: 0.8935 (p) REVERT: A 189 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6530 (mmmt) REVERT: B 632 ASP cc_start: 0.8862 (t70) cc_final: 0.8398 (t0) REVERT: B 657 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7827 (tp30) REVERT: B 660 LEU cc_start: 0.8228 (tt) cc_final: 0.7892 (tp) REVERT: C 46 LYS cc_start: 0.8823 (mmpt) cc_final: 0.8600 (mmtm) REVERT: D 632 ASP cc_start: 0.8848 (t70) cc_final: 0.8255 (t0) REVERT: D 656 ASN cc_start: 0.8152 (t0) cc_final: 0.7919 (t0) REVERT: E 35 TRP cc_start: 0.8237 (m-90) cc_final: 0.7874 (m100) REVERT: E 97 LYS cc_start: 0.8558 (mppt) cc_final: 0.8225 (mtmm) REVERT: E 207 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7828 (ptmt) REVERT: E 475 MET cc_start: 0.8493 (mmm) cc_final: 0.8254 (tpp) REVERT: F 588 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7424 (mtm110) REVERT: F 654 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7610 (mt-10) REVERT: F 655 LYS cc_start: 0.7893 (pttt) cc_final: 0.7527 (mtpt) REVERT: H 185 TYR cc_start: 0.7235 (m-80) cc_final: 0.6750 (m-80) REVERT: K 93 SER cc_start: 0.7967 (m) cc_final: 0.7510 (p) REVERT: L 3 GLN cc_start: 0.7793 (mp10) cc_final: 0.7469 (mp10) REVERT: L 66 ARG cc_start: 0.7365 (tpt90) cc_final: 0.6870 (tpt170) REVERT: L 76 LYS cc_start: 0.7924 (mppt) cc_final: 0.7478 (mptt) REVERT: L 81 GLU cc_start: 0.7688 (pm20) cc_final: 0.7391 (pm20) REVERT: L 100 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7141 (mp10) REVERT: L 103 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7598 (mtmm) REVERT: L 140 TYR cc_start: 0.6010 (t80) cc_final: 0.5783 (t80) outliers start: 52 outliers final: 37 residues processed: 304 average time/residue: 0.1504 time to fit residues: 69.3565 Evaluate side-chains 289 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 20 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN E 293 GLN J 6 GLN L 38 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107215 restraints weight = 29490.164| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.20 r_work: 0.3117 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 21221 Z= 0.340 Angle : 0.811 12.795 28989 Z= 0.394 Chirality : 0.050 0.257 3494 Planarity : 0.005 0.058 3533 Dihedral : 8.223 77.662 4309 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.84 % Allowed : 14.78 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.70 (0.17), residues: 2455 helix: -0.26 (0.25), residues: 463 sheet: -0.01 (0.20), residues: 737 loop : -0.75 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 192 TYR 0.019 0.002 TYR E 217 PHE 0.017 0.002 PHE A 376 TRP 0.013 0.002 TRP D 571 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00830 (21098) covalent geometry : angle 0.76681 (28663) SS BOND : bond 0.00756 ( 43) SS BOND : angle 2.91426 ( 86) hydrogen bonds : bond 0.04367 ( 617) hydrogen bonds : angle 5.37032 ( 1653) link_ALPHA1-2 : bond 0.00680 ( 2) link_ALPHA1-2 : angle 2.29407 ( 6) link_ALPHA1-3 : bond 0.00690 ( 6) link_ALPHA1-3 : angle 4.33253 ( 18) link_ALPHA1-6 : bond 0.00733 ( 4) link_ALPHA1-6 : angle 1.62241 ( 12) link_BETA1-2 : bond 0.00193 ( 2) link_BETA1-2 : angle 1.94678 ( 6) link_BETA1-4 : bond 0.00568 ( 25) link_BETA1-4 : angle 2.39070 ( 75) link_NAG-ASN : bond 0.00606 ( 41) link_NAG-ASN : angle 2.24325 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9383 (m) cc_final: 0.9022 (p) REVERT: A 189 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6587 (mmmt) REVERT: B 632 ASP cc_start: 0.8939 (t70) cc_final: 0.8472 (t0) REVERT: B 657 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7862 (tp30) REVERT: B 660 LEU cc_start: 0.8246 (tt) cc_final: 0.7910 (tp) REVERT: C 46 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8603 (mmtm) REVERT: C 116 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 265 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8680 (mp) REVERT: D 632 ASP cc_start: 0.8936 (t70) cc_final: 0.8597 (t0) REVERT: E 207 LYS cc_start: 0.8415 (mmtp) cc_final: 0.7943 (ptmt) REVERT: E 432 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: F 654 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7717 (mt-10) REVERT: F 655 LYS cc_start: 0.7906 (pttt) cc_final: 0.7591 (mtpt) REVERT: J 38 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6724 (ptp-170) REVERT: K 81 GLU cc_start: 0.7454 (pm20) cc_final: 0.7138 (pm20) REVERT: K 93 SER cc_start: 0.7952 (m) cc_final: 0.7487 (p) REVERT: L 3 GLN cc_start: 0.7831 (mp10) cc_final: 0.7523 (mp10) REVERT: L 76 LYS cc_start: 0.7941 (mppt) cc_final: 0.7480 (mptt) REVERT: L 100 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7193 (mp10) REVERT: L 103 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7636 (mtmm) REVERT: L 140 TYR cc_start: 0.6003 (t80) cc_final: 0.5770 (t80) outliers start: 62 outliers final: 41 residues processed: 308 average time/residue: 0.1601 time to fit residues: 74.9986 Evaluate side-chains 290 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 655 LYS 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 201 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 183 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 428 GLN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 425 ASN E 377 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.161983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112768 restraints weight = 29388.747| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.44 r_work: 0.3221 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21221 Z= 0.131 Angle : 0.658 12.119 28989 Z= 0.320 Chirality : 0.045 0.267 3494 Planarity : 0.004 0.048 3533 Dihedral : 7.286 65.906 4309 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.06 % Allowed : 16.06 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2455 helix: 0.22 (0.26), residues: 463 sheet: 0.15 (0.20), residues: 730 loop : -0.65 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.015 0.001 TYR B 638 PHE 0.011 0.001 PHE J 148 TRP 0.012 0.001 TRP C 69 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00298 (21098) covalent geometry : angle 0.61892 (28663) SS BOND : bond 0.00481 ( 43) SS BOND : angle 2.41034 ( 86) hydrogen bonds : bond 0.03451 ( 617) hydrogen bonds : angle 5.11684 ( 1653) link_ALPHA1-2 : bond 0.00152 ( 2) link_ALPHA1-2 : angle 1.99350 ( 6) link_ALPHA1-3 : bond 0.01159 ( 6) link_ALPHA1-3 : angle 4.17910 ( 18) link_ALPHA1-6 : bond 0.01076 ( 4) link_ALPHA1-6 : angle 0.96870 ( 12) link_BETA1-2 : bond 0.00238 ( 2) link_BETA1-2 : angle 2.09855 ( 6) link_BETA1-4 : bond 0.00537 ( 25) link_BETA1-4 : angle 2.07854 ( 75) link_NAG-ASN : bond 0.00213 ( 41) link_NAG-ASN : angle 1.72006 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9345 (m) cc_final: 0.8981 (p) REVERT: A 116 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 189 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6632 (mmmt) REVERT: B 632 ASP cc_start: 0.8816 (t70) cc_final: 0.8390 (t0) REVERT: B 657 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7879 (tp30) REVERT: B 658 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 660 LEU cc_start: 0.8252 (tt) cc_final: 0.7913 (tp) REVERT: C 46 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8610 (mmtm) REVERT: D 535 MET cc_start: 0.8905 (mmm) cc_final: 0.8592 (mtt) REVERT: D 632 ASP cc_start: 0.8808 (t70) cc_final: 0.8194 (t0) REVERT: E 35 TRP cc_start: 0.8373 (m-90) cc_final: 0.8016 (m100) REVERT: E 97 LYS cc_start: 0.8568 (mppt) cc_final: 0.8238 (mtmm) REVERT: E 166 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8106 (ttp80) REVERT: E 207 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7848 (ptmt) REVERT: E 432 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: F 530 MET cc_start: 0.8804 (mtp) cc_final: 0.8587 (mtp) REVERT: F 588 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7397 (mtm110) REVERT: F 654 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7758 (mt-10) REVERT: K 93 SER cc_start: 0.7827 (m) cc_final: 0.7397 (p) REVERT: L 3 GLN cc_start: 0.7760 (mp10) cc_final: 0.7500 (mp10) REVERT: L 76 LYS cc_start: 0.8034 (mppt) cc_final: 0.7614 (mptt) REVERT: L 82 ASP cc_start: 0.7745 (m-30) cc_final: 0.7299 (m-30) REVERT: L 100 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7288 (mp10) REVERT: L 103 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7706 (mtmm) REVERT: L 140 TYR cc_start: 0.6058 (t80) cc_final: 0.5841 (t80) outliers start: 45 outliers final: 34 residues processed: 301 average time/residue: 0.1606 time to fit residues: 72.4269 Evaluate side-chains 290 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 232 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 247 optimal weight: 30.0000 chunk 202 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN C 356 ASN E 377 ASN J 6 GLN L 38 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113317 restraints weight = 29363.994| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.11 r_work: 0.3224 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21221 Z= 0.128 Angle : 0.635 12.251 28989 Z= 0.308 Chirality : 0.044 0.251 3494 Planarity : 0.004 0.052 3533 Dihedral : 6.897 62.448 4309 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 16.70 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.32 (0.17), residues: 2455 helix: 0.54 (0.26), residues: 451 sheet: 0.02 (0.20), residues: 766 loop : -0.56 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.014 0.001 TYR K 49 PHE 0.019 0.001 PHE E 376 TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (21098) covalent geometry : angle 0.60030 (28663) SS BOND : bond 0.00395 ( 43) SS BOND : angle 2.10291 ( 86) hydrogen bonds : bond 0.03322 ( 617) hydrogen bonds : angle 4.97175 ( 1653) link_ALPHA1-2 : bond 0.00219 ( 2) link_ALPHA1-2 : angle 1.88929 ( 6) link_ALPHA1-3 : bond 0.01185 ( 6) link_ALPHA1-3 : angle 3.90011 ( 18) link_ALPHA1-6 : bond 0.01003 ( 4) link_ALPHA1-6 : angle 1.12237 ( 12) link_BETA1-2 : bond 0.00259 ( 2) link_BETA1-2 : angle 1.99255 ( 6) link_BETA1-4 : bond 0.00543 ( 25) link_BETA1-4 : angle 2.03014 ( 75) link_NAG-ASN : bond 0.00236 ( 41) link_NAG-ASN : angle 1.63359 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9424 (m) cc_final: 0.9039 (p) REVERT: A 189 LYS cc_start: 0.7327 (mmtt) cc_final: 0.6657 (mmmt) REVERT: B 632 ASP cc_start: 0.8953 (t70) cc_final: 0.8555 (t0) REVERT: B 657 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7854 (tp30) REVERT: B 658 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 660 LEU cc_start: 0.8144 (tt) cc_final: 0.7805 (tp) REVERT: C 46 LYS cc_start: 0.8949 (mmpt) cc_final: 0.8722 (mmtm) REVERT: C 166 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8335 (ttp80) REVERT: C 296 CYS cc_start: 0.6586 (m) cc_final: 0.6316 (m) REVERT: D 535 MET cc_start: 0.9064 (mmm) cc_final: 0.8801 (mtt) REVERT: D 632 ASP cc_start: 0.8952 (t70) cc_final: 0.8419 (t0) REVERT: E 35 TRP cc_start: 0.8405 (m-90) cc_final: 0.8035 (m100) REVERT: E 97 LYS cc_start: 0.8624 (mppt) cc_final: 0.8284 (mtmm) REVERT: E 166 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8271 (ttp80) REVERT: E 207 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7795 (ptmt) REVERT: E 432 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: F 530 MET cc_start: 0.8885 (mtp) cc_final: 0.8666 (mtp) REVERT: F 588 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7513 (mtm110) REVERT: F 654 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7843 (mt-10) REVERT: H 185 TYR cc_start: 0.7178 (m-80) cc_final: 0.6685 (m-80) REVERT: K 81 GLU cc_start: 0.7467 (pm20) cc_final: 0.7105 (pm20) REVERT: L 3 GLN cc_start: 0.7863 (mp10) cc_final: 0.7541 (mp10) REVERT: L 76 LYS cc_start: 0.8067 (mppt) cc_final: 0.7571 (mptt) REVERT: L 100 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7314 (mp10) REVERT: L 103 LYS cc_start: 0.8168 (mtmt) cc_final: 0.6945 (tttm) REVERT: L 140 TYR cc_start: 0.5971 (t80) cc_final: 0.5763 (t80) outliers start: 41 outliers final: 36 residues processed: 300 average time/residue: 0.1514 time to fit residues: 68.5504 Evaluate side-chains 294 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 224 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 142 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN C 356 ASN E 377 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113858 restraints weight = 29349.613| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.39 r_work: 0.3233 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21221 Z= 0.117 Angle : 0.619 12.382 28989 Z= 0.300 Chirality : 0.044 0.249 3494 Planarity : 0.004 0.050 3533 Dihedral : 6.610 59.784 4309 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.92 % Allowed : 16.61 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.23 (0.17), residues: 2455 helix: 0.78 (0.27), residues: 439 sheet: 0.09 (0.20), residues: 766 loop : -0.58 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.018 0.001 TYR H 91 PHE 0.019 0.001 PHE E 376 TRP 0.010 0.001 TRP E 112 HIS 0.002 0.001 HIS J 59 Details of bonding type rmsd covalent geometry : bond 0.00269 (21098) covalent geometry : angle 0.58798 (28663) SS BOND : bond 0.00386 ( 43) SS BOND : angle 1.95436 ( 86) hydrogen bonds : bond 0.03194 ( 617) hydrogen bonds : angle 4.84107 ( 1653) link_ALPHA1-2 : bond 0.00142 ( 2) link_ALPHA1-2 : angle 1.84858 ( 6) link_ALPHA1-3 : bond 0.01251 ( 6) link_ALPHA1-3 : angle 3.69416 ( 18) link_ALPHA1-6 : bond 0.01006 ( 4) link_ALPHA1-6 : angle 1.04989 ( 12) link_BETA1-2 : bond 0.00265 ( 2) link_BETA1-2 : angle 1.95913 ( 6) link_BETA1-4 : bond 0.00535 ( 25) link_BETA1-4 : angle 1.95367 ( 75) link_NAG-ASN : bond 0.00221 ( 41) link_NAG-ASN : angle 1.55244 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9398 (m) cc_final: 0.9011 (p) REVERT: A 116 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 189 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6578 (mmmt) REVERT: B 632 ASP cc_start: 0.8853 (t70) cc_final: 0.8441 (t0) REVERT: B 657 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7856 (tp30) REVERT: B 660 LEU cc_start: 0.8240 (tt) cc_final: 0.7960 (tp) REVERT: C 46 LYS cc_start: 0.8826 (mmpt) cc_final: 0.8624 (mmtm) REVERT: C 296 CYS cc_start: 0.5787 (m) cc_final: 0.5560 (m) REVERT: D 535 MET cc_start: 0.8872 (mmm) cc_final: 0.8629 (mtt) REVERT: D 632 ASP cc_start: 0.8797 (t70) cc_final: 0.8256 (t0) REVERT: E 35 TRP cc_start: 0.8330 (m-90) cc_final: 0.7954 (m100) REVERT: E 46 LYS cc_start: 0.8214 (pttp) cc_final: 0.7973 (mttm) REVERT: E 97 LYS cc_start: 0.8558 (mppt) cc_final: 0.8218 (mtmm) REVERT: E 166 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8102 (ttp80) REVERT: E 207 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7825 (ptmt) REVERT: E 432 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: F 530 MET cc_start: 0.8763 (mtp) cc_final: 0.8562 (mtp) REVERT: F 588 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7347 (mtm110) REVERT: H 12 LEU cc_start: 0.6997 (mm) cc_final: 0.6454 (tp) REVERT: H 185 TYR cc_start: 0.7163 (m-80) cc_final: 0.6609 (m-80) REVERT: L 3 GLN cc_start: 0.7755 (mp10) cc_final: 0.7472 (mp10) REVERT: L 39 MET cc_start: 0.7184 (mmm) cc_final: 0.6937 (tpt) REVERT: L 76 LYS cc_start: 0.8024 (mppt) cc_final: 0.7539 (mptt) REVERT: L 100 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7303 (mp10) REVERT: L 103 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7899 (mtmm) REVERT: L 140 TYR cc_start: 0.5983 (t80) cc_final: 0.5782 (t80) outliers start: 42 outliers final: 38 residues processed: 300 average time/residue: 0.1581 time to fit residues: 71.9646 Evaluate side-chains 300 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 428 GLN C 66 HIS C 356 ASN E 377 ASN J 6 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.161927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111746 restraints weight = 29635.560| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.32 r_work: 0.3198 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21221 Z= 0.169 Angle : 0.644 12.307 28989 Z= 0.313 Chirality : 0.045 0.243 3494 Planarity : 0.004 0.053 3533 Dihedral : 6.674 59.533 4309 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 2.01 % Allowed : 16.83 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.25 (0.17), residues: 2455 helix: 0.73 (0.27), residues: 437 sheet: 0.15 (0.20), residues: 749 loop : -0.62 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 504 TYR 0.017 0.001 TYR B 638 PHE 0.017 0.002 PHE E 376 TRP 0.010 0.001 TRP C 96 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00405 (21098) covalent geometry : angle 0.61250 (28663) SS BOND : bond 0.00442 ( 43) SS BOND : angle 2.08390 ( 86) hydrogen bonds : bond 0.03369 ( 617) hydrogen bonds : angle 4.88915 ( 1653) link_ALPHA1-2 : bond 0.00314 ( 2) link_ALPHA1-2 : angle 1.93876 ( 6) link_ALPHA1-3 : bond 0.01131 ( 6) link_ALPHA1-3 : angle 3.54885 ( 18) link_ALPHA1-6 : bond 0.00817 ( 4) link_ALPHA1-6 : angle 1.16657 ( 12) link_BETA1-2 : bond 0.00172 ( 2) link_BETA1-2 : angle 1.90403 ( 6) link_BETA1-4 : bond 0.00530 ( 25) link_BETA1-4 : angle 1.96863 ( 75) link_NAG-ASN : bond 0.00284 ( 41) link_NAG-ASN : angle 1.65494 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9399 (m) cc_final: 0.9048 (p) REVERT: A 116 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 189 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6579 (mmmt) REVERT: B 632 ASP cc_start: 0.8884 (t70) cc_final: 0.8471 (t0) REVERT: B 657 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7867 (tp30) REVERT: B 660 LEU cc_start: 0.8225 (tt) cc_final: 0.7949 (tp) REVERT: C 46 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8617 (mmtm) REVERT: C 296 CYS cc_start: 0.5831 (m) cc_final: 0.5602 (m) REVERT: D 535 MET cc_start: 0.8847 (mmm) cc_final: 0.8632 (mtt) REVERT: D 617 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8278 (mtp180) REVERT: D 632 ASP cc_start: 0.8838 (t70) cc_final: 0.8303 (t0) REVERT: E 35 TRP cc_start: 0.8312 (m-90) cc_final: 0.7940 (m100) REVERT: E 46 LYS cc_start: 0.8217 (pttp) cc_final: 0.8001 (mttm) REVERT: E 97 LYS cc_start: 0.8567 (mppt) cc_final: 0.8211 (mtmm) REVERT: E 207 LYS cc_start: 0.8363 (mmtp) cc_final: 0.7861 (ptmt) REVERT: E 432 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: F 530 MET cc_start: 0.8764 (mtp) cc_final: 0.8524 (mtp) REVERT: F 588 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7364 (mtm110) REVERT: H 12 LEU cc_start: 0.7015 (mm) cc_final: 0.6681 (mm) REVERT: H 66 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7257 (mtm-85) REVERT: H 185 TYR cc_start: 0.7199 (m-80) cc_final: 0.6661 (m-80) REVERT: K 81 GLU cc_start: 0.6884 (pm20) cc_final: 0.6600 (pm20) REVERT: L 3 GLN cc_start: 0.7768 (mp10) cc_final: 0.7481 (mp10) REVERT: L 76 LYS cc_start: 0.7982 (mppt) cc_final: 0.7442 (mptt) REVERT: L 100 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7302 (mp10) REVERT: L 103 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7915 (mtmm) REVERT: L 140 TYR cc_start: 0.6006 (t80) cc_final: 0.5803 (t80) outliers start: 44 outliers final: 40 residues processed: 297 average time/residue: 0.1432 time to fit residues: 64.8817 Evaluate side-chains 296 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 227 optimal weight: 30.0000 chunk 120 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110795 restraints weight = 29499.510| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.46 r_work: 0.3163 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21221 Z= 0.223 Angle : 0.688 12.574 28989 Z= 0.334 Chirality : 0.046 0.242 3494 Planarity : 0.004 0.057 3533 Dihedral : 6.896 62.698 4309 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.06 % Allowed : 16.65 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.37 (0.17), residues: 2455 helix: 0.43 (0.26), residues: 449 sheet: 0.15 (0.20), residues: 734 loop : -0.68 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 504 TYR 0.019 0.002 TYR B 638 PHE 0.022 0.002 PHE E 376 TRP 0.012 0.001 TRP C 69 HIS 0.013 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00541 (21098) covalent geometry : angle 0.65486 (28663) SS BOND : bond 0.00512 ( 43) SS BOND : angle 2.32712 ( 86) hydrogen bonds : bond 0.03564 ( 617) hydrogen bonds : angle 4.98400 ( 1653) link_ALPHA1-2 : bond 0.00426 ( 2) link_ALPHA1-2 : angle 2.02422 ( 6) link_ALPHA1-3 : bond 0.01044 ( 6) link_ALPHA1-3 : angle 3.47567 ( 18) link_ALPHA1-6 : bond 0.00790 ( 4) link_ALPHA1-6 : angle 1.25371 ( 12) link_BETA1-2 : bond 0.00239 ( 2) link_BETA1-2 : angle 1.94821 ( 6) link_BETA1-4 : bond 0.00526 ( 25) link_BETA1-4 : angle 2.02646 ( 75) link_NAG-ASN : bond 0.00362 ( 41) link_NAG-ASN : angle 1.76890 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.35 seconds wall clock time: 92 minutes 55.46 seconds (5575.46 seconds total)