Starting phenix.real_space_refine on Sun Aug 24 12:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8t_16493/08_2025/8c8t_16493.cif" } 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= -0.002 sd= 0.080 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 122 5.16 5 C 12469 2.51 5 N 3347 2.21 5 O 3824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19762 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3254 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 22, 'TRANS': 397} Chain breaks: 5 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 897 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3277 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3246 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 400} Chain breaks: 6 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 891 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 906 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 32 Chain: "J" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 879 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "T" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 680 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 89} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "U" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 664 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 92} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 5, 'GLU:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 773 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 773 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" 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: "G" 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: "T" 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: 4.46, per 1000 atoms: 0.23 Number of scatterers: 19762 At special positions: 0 Unit cell: (126.42, 141.04, 155.66, 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 122 16.00 O 3824 8.00 N 3347 7.00 C 12469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 100 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 332 " " NAG A 607 " - " ASN A 363 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 448 " " NAG E 1 " - " ASN A 156 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 197 " " NAG F 604 " - " ASN F 339 " " NAG F 605 " - " ASN F 448 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 88 " " NAG G 601 " - " ASN G 160 " " NAG G 602 " - " ASN G 197 " " NAG G 603 " - " ASN G 295 " " NAG G 604 " - " ASN G 448 " " NAG G 605 " - " ASN G 156 " " NAG G 606 " - " ASN G 332 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN F 295 " " NAG N 1 " - " ASN F 301 " " NAG O 1 " - " ASN F 332 " " NAG P 1 " - " ASN F 363 " " NAG Q 1 " - " ASN F 386 " " NAG T 301 " - " ASN T 72 " " NAG V 1 " - " ASN F 156 " " NAG W 1 " - " ASN F 276 " " NAG X 1 " - " ASN F 262 " " NAG Y 1 " - " ASN G 363 " " NAG Z 1 " - " ASN G 386 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 276 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 865.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 41 sheets defined 17.8% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.807A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.669A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' 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 483 removed outlier: 3.560A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.802A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.579A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 575 through 596 removed outlier: 3.717A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.685A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.791A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.868A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.797A pdb=" N ASP C 89 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.521A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.891A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.511A pdb=" N MET G 104 " --> pdb=" O MET G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.673A pdb=" N GLY G 343 " --> pdb=" O ASN G 339 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.582A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.548A pdb=" N ASP H 89 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.008A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 595 removed outlier: 3.932A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA I 578 " --> pdb=" O LYS I 574 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 583 " --> pdb=" O ARG I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.669A pdb=" N TRP I 623 " --> pdb=" O LEU I 619 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.699A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU I 634 " --> pdb=" O GLN I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 649 removed outlier: 3.847A pdb=" N GLU I 648 " --> pdb=" O GLY I 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 661 Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 543 removed outlier: 3.874A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 596 removed outlier: 3.662A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 626 removed outlier: 3.700A pdb=" N MET J 626 " --> pdb=" O ILE J 622 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 removed outlier: 3.847A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 651 through 662 removed outlier: 3.508A pdb=" N ALA J 662 " --> pdb=" O GLN J 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.636A pdb=" N ASP R 31 " --> pdb=" O ASN R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 65 Processing helix chain 'R' and resid 76 through 79 removed outlier: 4.062A pdb=" N ASP R 79 " --> pdb=" O TRP R 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 76 through 79' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.799A pdb=" N ASP S 31 " --> pdb=" O ASN S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 95 removed outlier: 4.107A pdb=" N THR S 95 " --> pdb=" O SER S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.634A pdb=" N ILE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 4.138A pdb=" N ILE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.709A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.909A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.928A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.927A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.764A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.448A 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 322 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 420 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.693A pdb=" N THR C 115 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 93 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 117 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 494 through 499 removed outlier: 4.459A pdb=" N VAL F 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.568A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 121 through 122 removed outlier: 4.016A pdb=" N ILE F 201 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR F 202 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 6.702A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 322 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 466 through 470 Processing sheet with id=AB9, first strand: chain 'G' and resid 498 through 499 removed outlier: 5.368A pdb=" N VAL J 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL G 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR J 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.872A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.585A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 307 through 312 removed outlier: 6.558A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.630A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 50 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AD2, first strand: chain 'R' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 11 current: chain 'R' and resid 45 through 51 removed outlier: 3.613A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 58 through 59 current: chain 'R' and resid 110 through 113 Processing sheet with id=AD3, first strand: chain 'R' and resid 18 through 24 removed outlier: 3.547A pdb=" N THR R 71 " --> pdb=" O TYR R 84 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 4 through 6 removed outlier: 3.656A pdb=" N SER S 82 " --> pdb=" O HIS S 73 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR S 71 " --> pdb=" O TYR S 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 11 current: chain 'S' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 45 through 51 current: chain 'S' and resid 110 through 113 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AD7, first strand: chain 'T' and resid 53 through 54 removed outlier: 5.703A pdb=" N LEU T 46 " --> pdb=" O GLN T 37 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN T 37 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE T 48 " --> pdb=" O TRP T 35 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.927A pdb=" N VAL U 19 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE U 75 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 21 " --> pdb=" O LEU U 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 10 through 12 current: chain 'U' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 45 through 48 current: chain 'U' and resid 97 through 98 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AE2, first strand: chain 'D' and resid 16 through 22 Processing sheet with id=AE3, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.398A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 8 through 10 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 8 through 10 current: chain 'K' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 46 through 49 current: chain 'K' and resid 98 through 99 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 17 through 22 removed outlier: 3.684A pdb=" N THR K 75 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER K 64 " --> pdb=" O THR K 75 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6265 1.35 - 1.47: 5348 1.47 - 1.60: 8413 1.60 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 20188 Sorted by residual: bond pdb=" C1 NAG T 301 " pdb=" O5 NAG T 301 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.363 -0.030 8.40e-03 1.42e+04 1.26e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.372 0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" C5 MAN V 4 " pdb=" O5 MAN V 4 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 NAG b 2 " pdb=" O5 NAG b 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 20183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 26781 1.89 - 3.78: 628 3.78 - 5.68: 77 5.68 - 7.57: 14 7.57 - 9.46: 1 Bond angle restraints: 27501 Sorted by residual: angle pdb=" C ASP K 51 " pdb=" N VAL K 52 " pdb=" CA VAL K 52 " ideal model delta sigma weight residual 121.97 128.84 -6.87 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C ARG H 28 " pdb=" N VAL H 29 " pdb=" CA VAL H 29 " ideal model delta sigma weight residual 121.97 127.74 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" N GLY S 49 " pdb=" CA GLY S 49 " pdb=" C GLY S 49 " ideal model delta sigma weight residual 111.85 115.22 -3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" CA GLY S 49 " pdb=" C GLY S 49 " pdb=" N TRP S 50 " ideal model delta sigma weight residual 114.23 116.93 -2.70 8.80e-01 1.29e+00 9.40e+00 angle pdb=" C ARG C 28 " pdb=" N VAL C 29 " pdb=" CA VAL C 29 " ideal model delta sigma weight residual 121.97 127.36 -5.39 1.80e+00 3.09e-01 8.97e+00 ... (remaining 27496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 11766 22.13 - 44.27: 732 44.27 - 66.40: 96 66.40 - 88.54: 42 88.54 - 110.67: 19 Dihedral angle restraints: 12655 sinusoidal: 5470 harmonic: 7185 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 100 " pdb=" CB CYS S 100 " ideal model delta sinusoidal sigma weight residual -86.00 -175.93 89.93 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -163.59 77.59 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -142.41 56.41 1 1.00e+01 1.00e-02 4.29e+01 ... (remaining 12652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 3273 0.179 - 0.358: 13 0.358 - 0.537: 0 0.537 - 0.717: 0 0.717 - 0.896: 1 Chirality restraints: 3287 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN F 363 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" C1 NAG T 301 " pdb=" ND2 ASN T 72 " pdb=" C2 NAG T 301 " pdb=" O5 NAG T 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG F 607 " pdb=" ND2 ASN F 88 " pdb=" C2 NAG F 607 " pdb=" O5 NAG F 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3284 not shown) Planarity restraints: 3462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 59 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO K 60 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO K 60 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 60 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 479 " -0.031 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP G 479 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP G 479 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP G 479 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 479 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 479 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 479 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 479 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 479 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 59 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO D 60 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " 0.041 5.00e-02 4.00e+02 ... (remaining 3459 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 398 2.69 - 3.24: 17901 3.24 - 3.79: 27804 3.79 - 4.35: 37190 4.35 - 4.90: 64475 Nonbonded interactions: 147768 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" O CYS J 604 " model vdw 2.135 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR J 606 " model vdw 2.166 3.040 nonbonded pdb=" OG SER C 15 " pdb=" OE1 GLU C 16 " model vdw 2.180 3.040 nonbonded pdb=" NE1 TRP C 47 " pdb=" O LEU D 98 " model vdw 2.207 3.120 nonbonded pdb=" NH2 ARG S 67 " pdb=" OD2 ASP S 94 " model vdw 2.255 3.120 ... (remaining 147763 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 45 or (resid 46 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 56 or resid 66 through \ 71 or (resid 72 through 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 77 or (resid 81 through 83 and (name N or name CA or nam \ e C or name O or name CB )) or resid 84 through 134 or (resid 135 through 151 an \ d (name N or name CA or name C or name O or name CB )) or resid 152 through 245 \ or (resid 246 and (name N or name CA or name C or name O or name CB )) or resid \ 247 through 321 or (resid 321A and (name N or name CA or name C or name O or nam \ e CB )) or resid 322 through 324 or (resid 325 and (name N or name CA or name C \ or name O or name CB )) or resid 326 through 395 or (resid 412 and (name N or na \ me CA or name C or name O or name CB )) or resid 413 through 429 or (resid 430 a \ nd (name N or name CA or name C or name O or name CB )) or resid 431 through 501 \ or (resid 502 and (name N or name CA or name C or name O or name CB )) or resid \ 503 or resid 602 through 607)) selection = (chain 'F' and (resid 34 through 46 or (resid 47 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 56 or resid 66 through \ 77 or resid 81 through 134 or (resid 135 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 150 through 151 and (name N or name CA or name C or \ name O or name CB )) or resid 152 through 228 or (resid 229 and (name N or name \ CA or name C or name O or name CB )) or resid 230 or (resid 231 through 232 and \ (name N or name CA or name C or name O or name CB )) or resid 233 through 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 0 through 321 or (resid 321A and (name N or name CA or name C or name O or name \ CB )) or resid 322 through 324 or (resid 325 and (name N or name CA or name C or \ name O or name CB )) or resid 326 through 355 or (resid 356 and (name N or name \ CA or name C or name O or name CB )) or resid 357 through 395 or resid 412 thro \ ugh 457 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 503 or resid 601 through 606)) selection = (chain 'G' and (resid 34 through 77 or (resid 81 through 83 and (name N or name \ CA or name C or name O or name CB )) or resid 84 through 184 or (resid 189 and ( \ name N or name CA or name C or name O or name CB )) or resid 190 through 210 or \ (resid 211 and (name N or name CA or name C or name O or name CB )) or resid 212 \ through 228 or (resid 229 and (name N or name CA or name C or name O or name CB \ )) or resid 230 or (resid 231 through 232 and (name N or name CA or name C or n \ ame O or name CB )) or resid 233 through 245 or (resid 246 and (name N or name C \ A or name C or name O or name CB )) or resid 247 through 268 or (resid 269 and ( \ name N or name CA or name C or name O or name CB )) or resid 270 through 395 or \ resid 412 through 457 or (resid 466 and (name N or name CA or name C or name O o \ r name CB )) or resid 467 through 503 or resid 601 through 606)) } ncs_group { reference = (chain 'B' and (resid 521 through 534 or (resid 535 and (name N or name CA or na \ me C or name O or name CB )) or resid 536 through 545 or resid 570 through 587 o \ r (resid 588 through 589 and (name N or name CA or name C or name O or name CB ) \ ) or resid 590 through 610 or (resid 616 through 621 and (name N or name CA or n \ ame C or name O or name CB )) or resid 622 through 624 or (resid 625 and (name N \ or name CA or name C or name O or name CB )) or resid 626 through 631 or (resid \ 632 through 633 and (name N or name CA or name C or name O or name CB )) or res \ id 634 through 647 or (resid 648 and (name N or name CA or name C or name O or n \ ame CB )) or resid 649 or (resid 650 and (name N or name CA or name C or name O \ or name CB )) or resid 651 through 653 or (resid 654 and (name N or name CA or n \ ame C or name O or name CB )) or resid 655 through 657 or (resid 658 and (name N \ or name CA or name C or name O or name CB )) or resid 659 through 660 or (resid \ 661 through 662 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 521 through 587 or (resid 588 through 589 and (name N or n \ ame CA or name C or name O or name CB )) or resid 590 through 610 or (resid 616 \ through 621 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 2 through 632 or (resid 633 and (name N or name CA or name C or name O or name C \ B )) or resid 634 through 636 or (resid 637 and (name N or name CA or name C or \ name O or name CB )) or resid 638 through 640 or (resid 641 and (name N or name \ CA or name C or name O or name CB )) or resid 642 through 660 or (resid 661 thro \ ugh 662 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 521 through 534 or (resid 535 and (name N or name CA or na \ me C or name O or name CB )) or resid 536 through 545 or resid 570 through 619 o \ r (resid 620 through 621 and (name N or name CA or name C or name O or name CB ) \ ) or resid 622 through 631 or (resid 632 through 633 and (name N or name CA or n \ ame C or name O or name CB )) or resid 634 through 636 or (resid 637 and (name N \ or name CA or name C or name O or name CB )) or resid 638 through 640 or (resid \ 641 and (name N or name CA or name C or name O or name CB )) or resid 642 throu \ gh 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) or \ resid 655 through 657 or (resid 658 and (name N or name CA or name C or name O \ or name CB )) or resid 659 through 662)) } ncs_group { reference = (chain 'C' and (resid 2 through 15 or (resid 16 through 17 and (name N or name C \ A or name C or name O or name CB )) or resid 18 through 120)) selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'L' selection = chain 'X' } ncs_group { reference = (chain 'R' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 61 or (resid 62 through 63 and (name \ N or name CA or name C or name O or name CB )) or resid 64 through 72 or (resid \ 73 through 74 and (name N or name CA or name C or name O or name CB )) or resid \ 75 through 76 or resid 81 through 90 or (resid 91 and (name N or name CA or nam \ e C or name O or name CB )) or resid 92 through 121)) selection = (chain 'S' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 121)) } ncs_group { reference = (chain 'T' and (resid 1 through 13 or (resid 14 through 15 and (name N or name C \ A or name C or name O or name CB )) or resid 16 through 37 or (resid 38 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 53 or (resid 54 through 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or name \ CB )) or resid 59 through 66 or (resid 67 and (name N or name CA or name C or na \ me O or name CB )) or (resid 68 through 70 and (name N or name CA or name C or n \ ame O or name CB )) or resid 71 through 78 or (resid 79 and (name N or name CA o \ r name C or name O or name CB )) or resid 80 through 82 or (resid 83 through 84 \ and (name N or name CA or name C or name O or name CB )) or resid 85 through 101 \ or (resid 102 through 103 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'U' and (resid 1 through 38 or (resid 39 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 or (resid 42 through 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 59 or (resi \ d 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throug \ h 73 or (resid 74 through 77 and (name N or name CA or name C or name O or name \ CB )) or resid 78 through 103)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.004 0.076 20281 Z= 0.187 Angle : 0.719 21.079 27741 Z= 0.348 Chirality : 0.052 0.896 3287 Planarity : 0.006 0.112 3424 Dihedral : 14.744 110.671 7915 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.17), residues: 2428 helix: -0.08 (0.28), residues: 375 sheet: 0.07 (0.17), residues: 847 loop : -0.69 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 75 TYR 0.018 0.001 TYR U 49 PHE 0.015 0.001 PHE G 223 TRP 0.067 0.002 TRP G 479 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00390 (20188) covalent geometry : angle 0.67018 (27501) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.08944 ( 72) hydrogen bonds : bond 0.17447 ( 501) hydrogen bonds : angle 6.77116 ( 1305) Misc. bond : bond 0.00171 ( 1) link_ALPHA1-3 : bond 0.00810 ( 1) link_ALPHA1-3 : angle 1.93912 ( 3) link_BETA1-4 : bond 0.00499 ( 17) link_BETA1-4 : angle 2.34365 ( 51) link_NAG-ASN : bond 0.00423 ( 38) link_NAG-ASN : angle 3.75062 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7436 (ttm170) REVERT: C 97 ARG cc_start: 0.7421 (ptm160) cc_final: 0.7152 (ptt90) REVERT: F 377 ASN cc_start: 0.7805 (p0) cc_final: 0.7445 (p0) REVERT: H 103 TRP cc_start: 0.6957 (p-90) cc_final: 0.6715 (p-90) REVERT: T 89 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7827 (pp30) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.1295 time to fit residues: 47.5822 Evaluate side-chains 201 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 543 ASN Chi-restraints excluded: chain T residue 89 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN H 77 GLN J 653 GLN S 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124059 restraints weight = 24699.123| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.60 r_work: 0.3187 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20281 Z= 0.195 Angle : 0.725 20.253 27741 Z= 0.349 Chirality : 0.052 0.836 3287 Planarity : 0.005 0.077 3424 Dihedral : 9.538 94.461 3830 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 7.41 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2428 helix: 0.11 (0.27), residues: 389 sheet: 0.03 (0.18), residues: 819 loop : -0.80 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 75 TYR 0.013 0.002 TYR U 49 PHE 0.015 0.002 PHE G 383 TRP 0.030 0.002 TRP G 479 HIS 0.009 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00480 (20188) covalent geometry : angle 0.67919 (27501) SS BOND : bond 0.00373 ( 36) SS BOND : angle 1.25673 ( 72) hydrogen bonds : bond 0.05222 ( 501) hydrogen bonds : angle 5.35279 ( 1305) Misc. bond : bond 0.00086 ( 1) link_ALPHA1-3 : bond 0.01575 ( 1) link_ALPHA1-3 : angle 0.79123 ( 3) link_BETA1-4 : bond 0.00586 ( 17) link_BETA1-4 : angle 2.30471 ( 51) link_NAG-ASN : bond 0.00446 ( 38) link_NAG-ASN : angle 3.64478 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 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 164 GLU cc_start: 0.7569 (pt0) cc_final: 0.6942 (pt0) REVERT: F 195 ASN cc_start: 0.8766 (p0) cc_final: 0.8548 (p0) REVERT: F 201 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8807 (mt) REVERT: F 377 ASN cc_start: 0.8335 (p0) cc_final: 0.7885 (p0) REVERT: H 20 LEU cc_start: 0.7050 (mt) cc_final: 0.6787 (mt) REVERT: R 104 ARG cc_start: 0.9105 (ttm170) cc_final: 0.8887 (ttm170) REVERT: S 102 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7946 (tmm-80) outliers start: 27 outliers final: 21 residues processed: 220 average time/residue: 0.1358 time to fit residues: 46.3950 Evaluate side-chains 213 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 475 MET Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 63 GLN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 213 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN B 653 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN G 99 ASN H 77 GLN I 543 ASN J 651 ASN S 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.159782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123177 restraints weight = 24853.932| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.39 r_work: 0.3129 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20281 Z= 0.220 Angle : 0.738 20.293 27741 Z= 0.354 Chirality : 0.053 0.882 3287 Planarity : 0.005 0.075 3424 Dihedral : 8.570 91.362 3825 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 2.00 % Allowed : 11.32 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.16), residues: 2428 helix: -0.02 (0.27), residues: 392 sheet: -0.12 (0.17), residues: 832 loop : -1.01 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 75 TYR 0.017 0.002 TYR U 49 PHE 0.015 0.002 PHE G 383 TRP 0.030 0.002 TRP A 35 HIS 0.008 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00549 (20188) covalent geometry : angle 0.69108 (27501) SS BOND : bond 0.00398 ( 36) SS BOND : angle 1.25998 ( 72) hydrogen bonds : bond 0.05407 ( 501) hydrogen bonds : angle 5.20692 ( 1305) Misc. bond : bond 0.00094 ( 1) link_ALPHA1-3 : bond 0.01597 ( 1) link_ALPHA1-3 : angle 0.89121 ( 3) link_BETA1-4 : bond 0.00456 ( 17) link_BETA1-4 : angle 2.41028 ( 51) link_NAG-ASN : bond 0.00383 ( 38) link_NAG-ASN : angle 3.67873 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7710 (pt0) cc_final: 0.7093 (pt0) REVERT: A 178 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7591 (tpt170) REVERT: B 542 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7994 (mtt90) REVERT: B 629 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6109 (tt) REVERT: C 97 ARG cc_start: 0.7324 (ptm160) cc_final: 0.7091 (ptt90) REVERT: H 20 LEU cc_start: 0.7179 (mt) cc_final: 0.6953 (mt) REVERT: R 104 ARG cc_start: 0.9264 (ttm170) cc_final: 0.8866 (ttm170) REVERT: S 102 ARG cc_start: 0.8295 (tmm-80) cc_final: 0.8056 (tmm-80) REVERT: S 104 ARG cc_start: 0.8262 (ptt180) cc_final: 0.8014 (ptt90) outliers start: 40 outliers final: 25 residues processed: 233 average time/residue: 0.1233 time to fit residues: 44.3051 Evaluate side-chains 225 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 191 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN B 653 GLN I 543 ASN D 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126297 restraints weight = 24625.532| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.33 r_work: 0.3204 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20281 Z= 0.123 Angle : 0.646 18.369 27741 Z= 0.304 Chirality : 0.049 0.766 3287 Planarity : 0.005 0.076 3424 Dihedral : 7.761 88.646 3825 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 2.45 % Allowed : 12.47 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.17), residues: 2428 helix: 0.36 (0.28), residues: 387 sheet: -0.03 (0.18), residues: 829 loop : -0.92 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.014 0.001 TYR A 173 PHE 0.010 0.001 PHE G 383 TRP 0.028 0.001 TRP A 35 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00290 (20188) covalent geometry : angle 0.60290 (27501) SS BOND : bond 0.00302 ( 36) SS BOND : angle 0.91485 ( 72) hydrogen bonds : bond 0.03986 ( 501) hydrogen bonds : angle 4.85549 ( 1305) Misc. bond : bond 0.00072 ( 1) link_ALPHA1-3 : bond 0.01489 ( 1) link_ALPHA1-3 : angle 0.90156 ( 3) link_BETA1-4 : bond 0.00459 ( 17) link_BETA1-4 : angle 2.13808 ( 51) link_NAG-ASN : bond 0.00369 ( 38) link_NAG-ASN : angle 3.36430 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7578 (pt0) cc_final: 0.7013 (pt0) REVERT: A 178 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7510 (tpt170) REVERT: B 655 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7832 (mttp) REVERT: C 97 ARG cc_start: 0.7239 (ptm160) cc_final: 0.6897 (ptt90) REVERT: G 37 THR cc_start: 0.8547 (t) cc_final: 0.8301 (p) REVERT: G 349 LEU cc_start: 0.8583 (mt) cc_final: 0.8360 (mt) REVERT: J 610 TRP cc_start: 0.5994 (m100) cc_final: 0.5684 (m100) REVERT: R 104 ARG cc_start: 0.9164 (ttm170) cc_final: 0.8698 (ttm170) outliers start: 49 outliers final: 37 residues processed: 246 average time/residue: 0.1310 time to fit residues: 50.5070 Evaluate side-chains 243 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 239 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN H 77 GLN I 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.163865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127487 restraints weight = 24642.885| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.35 r_work: 0.3232 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20281 Z= 0.110 Angle : 0.626 17.497 27741 Z= 0.294 Chirality : 0.048 0.739 3287 Planarity : 0.004 0.073 3424 Dihedral : 7.312 86.125 3825 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 2.55 % Allowed : 13.27 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2428 helix: 0.50 (0.28), residues: 388 sheet: 0.06 (0.18), residues: 831 loop : -0.88 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.015 0.001 TYR A 173 PHE 0.012 0.001 PHE T 87 TRP 0.020 0.001 TRP H 103 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00257 (20188) covalent geometry : angle 0.58463 (27501) SS BOND : bond 0.00263 ( 36) SS BOND : angle 0.82565 ( 72) hydrogen bonds : bond 0.03680 ( 501) hydrogen bonds : angle 4.66016 ( 1305) Misc. bond : bond 0.00074 ( 1) link_ALPHA1-3 : bond 0.01498 ( 1) link_ALPHA1-3 : angle 1.13536 ( 3) link_BETA1-4 : bond 0.00439 ( 17) link_BETA1-4 : angle 2.07537 ( 51) link_NAG-ASN : bond 0.00385 ( 38) link_NAG-ASN : angle 3.26496 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7529 (pt0) cc_final: 0.6940 (pt0) REVERT: A 178 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.7454 (tpt170) REVERT: B 653 GLN cc_start: 0.7706 (mt0) cc_final: 0.7479 (mt0) REVERT: B 655 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7768 (mttp) REVERT: C 75 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7563 (ttm170) REVERT: C 97 ARG cc_start: 0.7109 (ptm160) cc_final: 0.5873 (ptt90) REVERT: H 20 LEU cc_start: 0.7049 (mt) cc_final: 0.6802 (mt) REVERT: J 610 TRP cc_start: 0.6017 (m100) cc_final: 0.5758 (m100) REVERT: R 104 ARG cc_start: 0.9080 (ttm170) cc_final: 0.8350 (ttm170) REVERT: S 109 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8739 (p0) outliers start: 51 outliers final: 35 residues processed: 247 average time/residue: 0.1499 time to fit residues: 57.9936 Evaluate side-chains 245 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 230 optimal weight: 40.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125760 restraints weight = 24565.630| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.37 r_work: 0.3197 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20281 Z= 0.132 Angle : 0.644 17.766 27741 Z= 0.302 Chirality : 0.049 0.773 3287 Planarity : 0.004 0.072 3424 Dihedral : 7.169 84.146 3825 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.60 % Allowed : 14.17 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.17), residues: 2428 helix: 0.56 (0.28), residues: 387 sheet: 0.06 (0.18), residues: 829 loop : -0.92 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.016 0.001 TYR A 173 PHE 0.011 0.001 PHE G 383 TRP 0.022 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (20188) covalent geometry : angle 0.60260 (27501) SS BOND : bond 0.00322 ( 36) SS BOND : angle 1.01376 ( 72) hydrogen bonds : bond 0.03921 ( 501) hydrogen bonds : angle 4.65796 ( 1305) Misc. bond : bond 0.00082 ( 1) link_ALPHA1-3 : bond 0.01481 ( 1) link_ALPHA1-3 : angle 1.07046 ( 3) link_BETA1-4 : bond 0.00410 ( 17) link_BETA1-4 : angle 2.10025 ( 51) link_NAG-ASN : bond 0.00354 ( 38) link_NAG-ASN : angle 3.26703 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7561 (pt0) cc_final: 0.6949 (pt0) REVERT: A 178 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7495 (tpt170) REVERT: B 655 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7778 (mttp) REVERT: C 75 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7576 (ttm170) REVERT: C 97 ARG cc_start: 0.7214 (ptm160) cc_final: 0.5983 (ptt90) REVERT: G 445 CYS cc_start: 0.7539 (m) cc_final: 0.7206 (m) REVERT: I 661 LEU cc_start: 0.7358 (mm) cc_final: 0.6930 (tt) REVERT: J 610 TRP cc_start: 0.6053 (m100) cc_final: 0.5747 (m100) REVERT: S 3 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6866 (pp30) REVERT: S 109 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8742 (p0) outliers start: 52 outliers final: 44 residues processed: 241 average time/residue: 0.1510 time to fit residues: 56.9766 Evaluate side-chains 252 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 86 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 18 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 148 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN H 77 GLN I 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.159674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122813 restraints weight = 24757.901| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.45 r_work: 0.3163 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20281 Z= 0.199 Angle : 0.713 19.429 27741 Z= 0.339 Chirality : 0.053 0.886 3287 Planarity : 0.005 0.073 3424 Dihedral : 7.368 83.676 3825 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 3.10 % Allowed : 13.92 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.17), residues: 2428 helix: 0.34 (0.27), residues: 386 sheet: -0.09 (0.18), residues: 829 loop : -1.10 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 166 TYR 0.017 0.002 TYR A 173 PHE 0.015 0.002 PHE G 383 TRP 0.027 0.002 TRP H 103 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00497 (20188) covalent geometry : angle 0.66760 (27501) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.29275 ( 72) hydrogen bonds : bond 0.04798 ( 501) hydrogen bonds : angle 4.86923 ( 1305) Misc. bond : bond 0.00101 ( 1) link_ALPHA1-3 : bond 0.01446 ( 1) link_ALPHA1-3 : angle 1.17913 ( 3) link_BETA1-4 : bond 0.00401 ( 17) link_BETA1-4 : angle 2.26539 ( 51) link_NAG-ASN : bond 0.00411 ( 38) link_NAG-ASN : angle 3.57889 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7695 (pt0) cc_final: 0.7081 (pt0) REVERT: A 178 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7521 (tpt170) REVERT: B 542 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7259 (mtt180) REVERT: B 653 GLN cc_start: 0.7985 (mt0) cc_final: 0.7783 (mt0) REVERT: B 655 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7870 (mttp) REVERT: C 97 ARG cc_start: 0.7292 (ptm160) cc_final: 0.6984 (ptt90) REVERT: G 164 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6421 (pp20) REVERT: G 445 CYS cc_start: 0.7557 (m) cc_final: 0.7225 (m) REVERT: S 3 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6891 (pp30) REVERT: S 104 ARG cc_start: 0.8261 (ptt180) cc_final: 0.8043 (ptt90) REVERT: S 109 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8787 (p0) outliers start: 62 outliers final: 48 residues processed: 238 average time/residue: 0.1545 time to fit residues: 57.0919 Evaluate side-chains 245 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 215 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 218 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 230 optimal weight: 40.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123840 restraints weight = 24663.810| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.41 r_work: 0.3178 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20281 Z= 0.168 Angle : 0.682 18.971 27741 Z= 0.322 Chirality : 0.051 0.838 3287 Planarity : 0.005 0.074 3424 Dihedral : 7.289 82.996 3825 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 2.95 % Allowed : 14.57 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2428 helix: 0.35 (0.27), residues: 386 sheet: -0.08 (0.18), residues: 815 loop : -1.11 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.017 0.001 TYR A 173 PHE 0.013 0.001 PHE G 383 TRP 0.029 0.001 TRP H 103 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00414 (20188) covalent geometry : angle 0.63847 (27501) SS BOND : bond 0.00350 ( 36) SS BOND : angle 1.09317 ( 72) hydrogen bonds : bond 0.04368 ( 501) hydrogen bonds : angle 4.80058 ( 1305) Misc. bond : bond 0.00083 ( 1) link_ALPHA1-3 : bond 0.01356 ( 1) link_ALPHA1-3 : angle 1.21659 ( 3) link_BETA1-4 : bond 0.00417 ( 17) link_BETA1-4 : angle 2.17015 ( 51) link_NAG-ASN : bond 0.00363 ( 38) link_NAG-ASN : angle 3.47304 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7644 (pt0) cc_final: 0.6996 (pt0) REVERT: A 178 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7527 (tpt170) REVERT: B 655 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7780 (mttp) REVERT: C 75 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7759 (ttm170) REVERT: C 97 ARG cc_start: 0.7277 (ptm160) cc_final: 0.6010 (ptt90) REVERT: C 104 ARG cc_start: 0.7121 (ptm160) cc_final: 0.6832 (ptm-80) REVERT: G 123 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7993 (p) REVERT: G 164 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6392 (pp20) REVERT: G 445 CYS cc_start: 0.7525 (m) cc_final: 0.7205 (m) REVERT: I 661 LEU cc_start: 0.7391 (mm) cc_final: 0.6977 (tt) REVERT: S 3 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6897 (pp30) REVERT: S 104 ARG cc_start: 0.8302 (ptt180) cc_final: 0.8055 (ptt90) REVERT: S 109 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8789 (p0) outliers start: 59 outliers final: 49 residues processed: 235 average time/residue: 0.1518 time to fit residues: 55.6328 Evaluate side-chains 246 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 87 optimal weight: 0.3980 chunk 143 optimal weight: 0.8980 chunk 197 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 187 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN I 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126865 restraints weight = 24483.466| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.39 r_work: 0.3224 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20281 Z= 0.101 Angle : 0.623 17.303 27741 Z= 0.291 Chirality : 0.048 0.707 3287 Planarity : 0.004 0.073 3424 Dihedral : 6.985 80.703 3825 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % Rotamer: Outliers : 1.90 % Allowed : 15.77 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.17), residues: 2428 helix: 0.61 (0.28), residues: 385 sheet: 0.13 (0.18), residues: 818 loop : -0.98 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.016 0.001 TYR A 173 PHE 0.012 0.001 PHE C 108 TRP 0.029 0.001 TRP H 103 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00228 (20188) covalent geometry : angle 0.58232 (27501) SS BOND : bond 0.00346 ( 36) SS BOND : angle 0.91513 ( 72) hydrogen bonds : bond 0.03432 ( 501) hydrogen bonds : angle 4.55185 ( 1305) Misc. bond : bond 0.00062 ( 1) link_ALPHA1-3 : bond 0.01183 ( 1) link_ALPHA1-3 : angle 1.41647 ( 3) link_BETA1-4 : bond 0.00448 ( 17) link_BETA1-4 : angle 1.98319 ( 51) link_NAG-ASN : bond 0.00382 ( 38) link_NAG-ASN : angle 3.19561 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7507 (pt0) cc_final: 0.6839 (pt0) REVERT: A 178 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7506 (tpt170) REVERT: B 542 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7175 (mtt180) REVERT: B 655 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7754 (mttp) REVERT: C 75 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7747 (ttm170) REVERT: C 97 ARG cc_start: 0.7207 (ptm160) cc_final: 0.6098 (ptt90) REVERT: C 104 ARG cc_start: 0.7099 (ptm160) cc_final: 0.6857 (ptm-80) REVERT: G 123 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7912 (p) REVERT: G 178 ARG cc_start: 0.8517 (tpt90) cc_final: 0.8268 (tpt90) REVERT: G 445 CYS cc_start: 0.7486 (m) cc_final: 0.7145 (m) REVERT: H 104 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7920 (mtp180) REVERT: I 661 LEU cc_start: 0.7453 (mm) cc_final: 0.7060 (tt) REVERT: S 3 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6896 (pp30) REVERT: S 109 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8744 (p0) outliers start: 38 outliers final: 31 residues processed: 222 average time/residue: 0.1631 time to fit residues: 55.3568 Evaluate side-chains 230 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN H 77 GLN I 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125017 restraints weight = 24701.741| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.43 r_work: 0.3198 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20281 Z= 0.157 Angle : 0.667 18.088 27741 Z= 0.314 Chirality : 0.051 0.804 3287 Planarity : 0.004 0.072 3424 Dihedral : 7.030 78.965 3825 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.05 % Allowed : 15.77 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.17), residues: 2428 helix: 0.53 (0.27), residues: 384 sheet: 0.02 (0.18), residues: 826 loop : -1.03 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.017 0.001 TYR A 173 PHE 0.014 0.001 PHE A 93 TRP 0.031 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00386 (20188) covalent geometry : angle 0.62598 (27501) SS BOND : bond 0.00352 ( 36) SS BOND : angle 1.12639 ( 72) hydrogen bonds : bond 0.04121 ( 501) hydrogen bonds : angle 4.67547 ( 1305) Misc. bond : bond 0.00091 ( 1) link_ALPHA1-3 : bond 0.01188 ( 1) link_ALPHA1-3 : angle 1.35570 ( 3) link_BETA1-4 : bond 0.00392 ( 17) link_BETA1-4 : angle 2.12090 ( 51) link_NAG-ASN : bond 0.00391 ( 38) link_NAG-ASN : angle 3.29808 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7594 (pt0) cc_final: 0.6941 (pt0) REVERT: A 178 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7515 (tpt170) REVERT: B 535 MET cc_start: 0.7886 (mtp) cc_final: 0.7492 (mmp) REVERT: B 542 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7194 (mtt180) REVERT: B 655 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7776 (mttp) REVERT: C 75 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7756 (ttm170) REVERT: C 97 ARG cc_start: 0.7241 (ptm160) cc_final: 0.6095 (ptt90) REVERT: C 104 ARG cc_start: 0.7110 (ptm160) cc_final: 0.6882 (ptm-80) REVERT: G 123 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7974 (p) REVERT: G 445 CYS cc_start: 0.7513 (m) cc_final: 0.7184 (m) REVERT: I 661 LEU cc_start: 0.7429 (mm) cc_final: 0.7017 (tt) REVERT: S 3 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6909 (pp30) REVERT: S 109 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8756 (p0) outliers start: 41 outliers final: 36 residues processed: 224 average time/residue: 0.1542 time to fit residues: 53.7125 Evaluate side-chains 234 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 96 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 208 optimal weight: 0.0980 chunk 219 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124246 restraints weight = 24688.317| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.38 r_work: 0.3195 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20281 Z= 0.154 Angle : 0.665 18.246 27741 Z= 0.313 Chirality : 0.050 0.806 3287 Planarity : 0.004 0.073 3424 Dihedral : 7.043 77.287 3825 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 2.30 % Allowed : 15.62 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2428 helix: 0.49 (0.27), residues: 385 sheet: 0.06 (0.18), residues: 803 loop : -1.06 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.017 0.001 TYR A 173 PHE 0.013 0.001 PHE A 93 TRP 0.032 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00377 (20188) covalent geometry : angle 0.62292 (27501) SS BOND : bond 0.00358 ( 36) SS BOND : angle 1.10544 ( 72) hydrogen bonds : bond 0.04114 ( 501) hydrogen bonds : angle 4.69035 ( 1305) Misc. bond : bond 0.00086 ( 1) link_ALPHA1-3 : bond 0.01145 ( 1) link_ALPHA1-3 : angle 1.37239 ( 3) link_BETA1-4 : bond 0.00408 ( 17) link_BETA1-4 : angle 2.10869 ( 51) link_NAG-ASN : bond 0.00377 ( 38) link_NAG-ASN : angle 3.33122 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5407.91 seconds wall clock time: 93 minutes 18.67 seconds (5598.67 seconds total)