Starting phenix.real_space_refine on Tue Jun 17 11:32:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8t_16493/06_2025/8c8t_16493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8t_16493/06_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_16493/06_2025/8c8t_16493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8t_16493/06_2025/8c8t_16493.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8t_16493/06_2025/8c8t_16493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8t_16493/06_2025/8c8t_16493.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, '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: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2} 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, 'PHE:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP: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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2} 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: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} 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: 13.90, per 1000 atoms: 0.70 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: 5.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.52 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: 6.69 Time building geometry restraints manager: 6.11 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: 5.440 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 48.660 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.720 ------------------------------------------------------------------------------- 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 : 5.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.067 0.002 TRP G 479 HIS 0.005 0.001 HIS F 374 PHE 0.015 0.001 PHE G 223 TYR 0.018 0.001 TYR U 49 ARG 0.013 0.000 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 38) link_NAG-ASN : angle 3.75062 ( 114) link_BETA1-4 : bond 0.00499 ( 17) link_BETA1-4 : angle 2.34365 ( 51) link_ALPHA1-3 : bond 0.00810 ( 1) link_ALPHA1-3 : angle 1.93912 ( 3) hydrogen bonds : bond 0.17447 ( 501) hydrogen bonds : angle 6.77116 ( 1305) SS BOND : bond 0.00338 ( 36) SS BOND : angle 1.08944 ( 72) covalent geometry : bond 0.00390 (20188) covalent geometry : angle 0.67018 (27501) Misc. bond : bond 0.00171 ( 1) *********************** 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 : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7435 (ttm170) 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: 0.3210 time to fit residues: 117.7730 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 : 2.030 ------------------------------------------------------------------------------- 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 204 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.166447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130107 restraints weight = 24502.825| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.30 r_work: 0.3241 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0888 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= 0.139 Angle : 0.668 18.992 27741 Z= 0.319 Chirality : 0.050 0.760 3287 Planarity : 0.005 0.077 3424 Dihedral : 9.432 94.557 3830 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 1.05 % Allowed : 7.01 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2428 helix: 0.31 (0.28), residues: 388 sheet: 0.12 (0.18), residues: 812 loop : -0.67 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 479 HIS 0.006 0.001 HIS F 374 PHE 0.011 0.001 PHE G 383 TYR 0.010 0.001 TYR U 49 ARG 0.006 0.001 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 38) link_NAG-ASN : angle 3.41778 ( 114) link_BETA1-4 : bond 0.00429 ( 17) link_BETA1-4 : angle 2.17688 ( 51) link_ALPHA1-3 : bond 0.01622 ( 1) link_ALPHA1-3 : angle 0.89736 ( 3) hydrogen bonds : bond 0.04504 ( 501) hydrogen bonds : angle 5.22310 ( 1305) SS BOND : bond 0.00293 ( 36) SS BOND : angle 0.99591 ( 72) covalent geometry : bond 0.00325 (20188) covalent geometry : angle 0.62465 (27501) Misc. bond : bond 0.00076 ( 1) *********************** 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 223 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7577 (pt0) cc_final: 0.6997 (pt0) REVERT: F 195 ASN cc_start: 0.8634 (p0) cc_final: 0.8387 (p0) REVERT: F 377 ASN cc_start: 0.8273 (p0) cc_final: 0.7847 (p0) REVERT: G 349 LEU cc_start: 0.8495 (tp) cc_final: 0.8280 (mt) REVERT: R 104 ARG cc_start: 0.9192 (ttm170) cc_final: 0.8981 (ttm170) REVERT: U 33 LEU cc_start: 0.8389 (tt) cc_final: 0.8139 (tt) outliers start: 21 outliers final: 16 residues processed: 213 average time/residue: 0.3073 time to fit residues: 101.8681 Evaluate side-chains 203 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 450 THR Chi-restraints excluded: chain I residue 592 LEU 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 223 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 653 GLN G 99 ASN H 77 GLN I 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119175 restraints weight = 24556.150| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.66 r_work: 0.3117 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20281 Z= 0.292 Angle : 0.828 22.235 27741 Z= 0.402 Chirality : 0.057 0.973 3287 Planarity : 0.006 0.075 3424 Dihedral : 8.897 91.690 3825 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 2.35 % Allowed : 10.82 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2428 helix: -0.23 (0.26), residues: 397 sheet: -0.24 (0.18), residues: 823 loop : -1.06 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 50 HIS 0.010 0.002 HIS F 374 PHE 0.019 0.002 PHE G 383 TYR 0.031 0.002 TYR A 191 ARG 0.005 0.001 ARG G 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 38) link_NAG-ASN : angle 4.01144 ( 114) link_BETA1-4 : bond 0.00502 ( 17) link_BETA1-4 : angle 2.65188 ( 51) link_ALPHA1-3 : bond 0.01605 ( 1) link_ALPHA1-3 : angle 0.90989 ( 3) hydrogen bonds : bond 0.06347 ( 501) hydrogen bonds : angle 5.42335 ( 1305) SS BOND : bond 0.00505 ( 36) SS BOND : angle 1.55228 ( 72) covalent geometry : bond 0.00732 (20188) covalent geometry : angle 0.77850 (27501) Misc. bond : bond 0.00084 ( 1) *********************** 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 255 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7267 (tpt170) REVERT: B 542 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7760 (mtt90) REVERT: B 629 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5686 (tt) REVERT: B 653 GLN cc_start: 0.7603 (mt0) cc_final: 0.7394 (mt0) REVERT: F 121 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8418 (mttm) REVERT: F 201 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8959 (mt) REVERT: H 38 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.7016 (tmm-80) REVERT: R 104 ARG cc_start: 0.9116 (ttm170) cc_final: 0.8524 (ttm110) REVERT: S 102 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7966 (tmm-80) REVERT: S 104 ARG cc_start: 0.8242 (ptt180) cc_final: 0.7849 (ptt90) REVERT: T 23 CYS cc_start: 0.7054 (p) cc_final: 0.6677 (p) outliers start: 47 outliers final: 30 residues processed: 236 average time/residue: 0.3200 time to fit residues: 115.9699 Evaluate side-chains 237 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 184 ILE 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 201 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 71 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 649 SER Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain J residue 657 GLU 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 Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 57 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN F 478 ASN H 77 GLN I 543 ASN S 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124774 restraints weight = 24694.207| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.45 r_work: 0.3191 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20281 Z= 0.137 Angle : 0.669 19.267 27741 Z= 0.316 Chirality : 0.050 0.810 3287 Planarity : 0.005 0.078 3424 Dihedral : 8.016 89.254 3825 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 2.20 % Allowed : 12.92 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2428 helix: 0.17 (0.27), residues: 393 sheet: -0.15 (0.18), residues: 818 loop : -1.00 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 35 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE G 383 TYR 0.011 0.001 TYR A 173 ARG 0.006 0.000 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 38) link_NAG-ASN : angle 3.52280 ( 114) link_BETA1-4 : bond 0.00470 ( 17) link_BETA1-4 : angle 2.21349 ( 51) link_ALPHA1-3 : bond 0.01464 ( 1) link_ALPHA1-3 : angle 0.85918 ( 3) hydrogen bonds : bond 0.04373 ( 501) hydrogen bonds : angle 4.97080 ( 1305) SS BOND : bond 0.00309 ( 36) SS BOND : angle 0.95356 ( 72) covalent geometry : bond 0.00327 (20188) covalent geometry : angle 0.62343 (27501) Misc. bond : bond 0.00077 ( 1) *********************** 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 260 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7470 (m-10) cc_final: 0.7150 (m-10) REVERT: A 164 GLU cc_start: 0.7602 (pt0) cc_final: 0.6995 (pt0) REVERT: A 178 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7511 (tpt170) REVERT: B 542 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7853 (mtt90) REVERT: B 629 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.6043 (tt) REVERT: B 653 GLN cc_start: 0.7617 (mt0) cc_final: 0.7400 (mt0) REVERT: B 655 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7853 (mttp) REVERT: C 97 ARG cc_start: 0.6954 (ptt90) cc_final: 0.5944 (ptt90) REVERT: G 173 TYR cc_start: 0.9145 (p90) cc_final: 0.8935 (p90) REVERT: H 38 ARG cc_start: 0.7432 (tmm-80) cc_final: 0.7194 (tmm-80) REVERT: R 104 ARG cc_start: 0.9179 (ttm170) cc_final: 0.8660 (ttm170) outliers start: 44 outliers final: 33 residues processed: 242 average time/residue: 0.3255 time to fit residues: 123.5990 Evaluate side-chains 238 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 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 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 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 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 71 THR 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 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 641 ILE Chi-restraints excluded: chain J residue 657 GLU 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 115 SER Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain T residue 96 GLU 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 189 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.162274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125894 restraints weight = 24752.353| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.43 r_work: 0.3208 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20281 Z= 0.126 Angle : 0.648 18.112 27741 Z= 0.305 Chirality : 0.049 0.779 3287 Planarity : 0.005 0.075 3424 Dihedral : 7.432 86.866 3825 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.68 % Rotamer: Outliers : 2.70 % Allowed : 13.47 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2428 helix: 0.47 (0.28), residues: 386 sheet: -0.10 (0.18), residues: 829 loop : -0.95 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE T 87 TYR 0.016 0.001 TYR A 173 ARG 0.006 0.000 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 38) link_NAG-ASN : angle 3.34442 ( 114) link_BETA1-4 : bond 0.00434 ( 17) link_BETA1-4 : angle 2.13876 ( 51) link_ALPHA1-3 : bond 0.01497 ( 1) link_ALPHA1-3 : angle 1.10917 ( 3) hydrogen bonds : bond 0.03983 ( 501) hydrogen bonds : angle 4.76126 ( 1305) SS BOND : bond 0.00272 ( 36) SS BOND : angle 0.89358 ( 72) covalent geometry : bond 0.00302 (20188) covalent geometry : angle 0.60514 (27501) Misc. bond : bond 0.00074 ( 1) *********************** 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 265 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7554 (pt0) cc_final: 0.6951 (pt0) REVERT: A 178 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7475 (tpt170) REVERT: B 629 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.6026 (tt) REVERT: B 653 GLN cc_start: 0.7479 (mt0) cc_final: 0.7228 (mt0) REVERT: B 655 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7725 (mttp) REVERT: C 75 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7544 (ttm170) REVERT: G 173 TYR cc_start: 0.9206 (p90) cc_final: 0.8954 (p90) REVERT: R 104 ARG cc_start: 0.9141 (ttm170) cc_final: 0.8517 (ttm170) REVERT: S 3 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6919 (pp30) REVERT: S 109 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8739 (p0) outliers start: 54 outliers final: 39 residues processed: 242 average time/residue: 0.3006 time to fit residues: 113.6503 Evaluate side-chains 247 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 2.873 ------------------------------------------------------------------------------- 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 535 MET 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 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 71 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 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 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 J residue 657 GLU 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 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 99 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 191 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN H 77 GLN I 543 ASN J 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123235 restraints weight = 24795.268| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.44 r_work: 0.3158 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20281 Z= 0.186 Angle : 0.702 19.097 27741 Z= 0.332 Chirality : 0.052 0.859 3287 Planarity : 0.005 0.075 3424 Dihedral : 7.453 85.542 3825 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 3.05 % Allowed : 14.17 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2428 helix: 0.32 (0.27), residues: 386 sheet: -0.15 (0.18), residues: 828 loop : -1.09 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 103 HIS 0.005 0.001 HIS F 374 PHE 0.014 0.002 PHE G 383 TYR 0.016 0.001 TYR A 173 ARG 0.005 0.000 ARG C 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 38) link_NAG-ASN : angle 3.55025 ( 114) link_BETA1-4 : bond 0.00412 ( 17) link_BETA1-4 : angle 2.24653 ( 51) link_ALPHA1-3 : bond 0.01450 ( 1) link_ALPHA1-3 : angle 1.01132 ( 3) hydrogen bonds : bond 0.04626 ( 501) hydrogen bonds : angle 4.87801 ( 1305) SS BOND : bond 0.00360 ( 36) SS BOND : angle 1.21281 ( 72) covalent geometry : bond 0.00461 (20188) covalent geometry : angle 0.65638 (27501) Misc. bond : bond 0.00100 ( 1) *********************** 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 268 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7674 (pt0) cc_final: 0.7054 (pt0) REVERT: A 178 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7497 (tpt170) REVERT: B 629 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6003 (tt) REVERT: B 655 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7838 (mttp) REVERT: C 75 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7594 (ttm170) REVERT: G 164 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6403 (pp20) REVERT: G 173 TYR cc_start: 0.9211 (p90) cc_final: 0.8955 (p90) REVERT: G 445 CYS cc_start: 0.7579 (m) cc_final: 0.7241 (m) REVERT: R 104 ARG cc_start: 0.9158 (ttm170) cc_final: 0.8491 (ttm170) REVERT: S 3 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6910 (pp30) REVERT: S 104 ARG cc_start: 0.8273 (ptt180) cc_final: 0.8041 (ptt90) REVERT: S 109 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8772 (p0) outliers start: 61 outliers final: 48 residues processed: 244 average time/residue: 0.4360 time to fit residues: 168.3519 Evaluate side-chains 254 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 3.327 ------------------------------------------------------------------------------- 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 426 MET 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 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 245 VAL 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 71 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 71 ILE Chi-restraints excluded: chain I residue 543 ASN 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 J residue 657 GLU 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 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 K residue 71 THR 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 170 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 229 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125945 restraints weight = 24554.919| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1928 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= 0.118 Angle : 0.647 18.063 27741 Z= 0.303 Chirality : 0.049 0.764 3287 Planarity : 0.004 0.075 3424 Dihedral : 7.231 84.163 3825 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 2.55 % Allowed : 15.07 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2428 helix: 0.50 (0.28), residues: 386 sheet: -0.08 (0.18), residues: 829 loop : -1.00 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 103 HIS 0.003 0.001 HIS A 249 PHE 0.011 0.001 PHE T 87 TYR 0.015 0.001 TYR A 173 ARG 0.004 0.000 ARG I 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 38) link_NAG-ASN : angle 3.43550 ( 114) link_BETA1-4 : bond 0.00423 ( 17) link_BETA1-4 : angle 2.08559 ( 51) link_ALPHA1-3 : bond 0.01329 ( 1) link_ALPHA1-3 : angle 1.15841 ( 3) hydrogen bonds : bond 0.03855 ( 501) hydrogen bonds : angle 4.69485 ( 1305) SS BOND : bond 0.00291 ( 36) SS BOND : angle 0.95507 ( 72) covalent geometry : bond 0.00277 (20188) covalent geometry : angle 0.60220 (27501) Misc. bond : bond 0.00074 ( 1) *********************** 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 258 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7561 (pt0) cc_final: 0.6911 (pt0) REVERT: A 178 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7499 (tpt170) REVERT: B 629 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6075 (tt) REVERT: B 653 GLN cc_start: 0.8000 (mt0) cc_final: 0.7725 (mt0) REVERT: B 655 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7797 (mttp) REVERT: C 75 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7575 (ttm170) REVERT: C 104 ARG cc_start: 0.6941 (ptm160) cc_final: 0.6574 (ptm160) REVERT: G 173 TYR cc_start: 0.9207 (p90) cc_final: 0.8974 (p90) REVERT: G 445 CYS cc_start: 0.7514 (m) cc_final: 0.7174 (m) REVERT: I 661 LEU cc_start: 0.7384 (mm) cc_final: 0.6950 (tt) REVERT: R 104 ARG cc_start: 0.9121 (ttm170) cc_final: 0.8535 (ttm170) REVERT: S 3 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6929 (pp30) REVERT: S 109 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8736 (p0) outliers start: 51 outliers final: 46 residues processed: 240 average time/residue: 0.3116 time to fit residues: 117.5369 Evaluate side-chains 252 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 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 71 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 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 J residue 657 GLU Chi-restraints excluded: chain R residue 2 VAL 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 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 D residue 107 THR Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 205 optimal weight: 30.0000 chunk 173 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.161077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124610 restraints weight = 24757.411| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.41 r_work: 0.3191 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20281 Z= 0.149 Angle : 0.663 18.230 27741 Z= 0.312 Chirality : 0.050 0.806 3287 Planarity : 0.004 0.073 3424 Dihedral : 7.163 82.894 3825 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 3.05 % Allowed : 14.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2428 helix: 0.45 (0.27), residues: 387 sheet: -0.08 (0.18), residues: 829 loop : -1.06 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 PHE 0.012 0.001 PHE G 383 TYR 0.016 0.001 TYR A 173 ARG 0.004 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 38) link_NAG-ASN : angle 3.38948 ( 114) link_BETA1-4 : bond 0.00404 ( 17) link_BETA1-4 : angle 2.13781 ( 51) link_ALPHA1-3 : bond 0.01415 ( 1) link_ALPHA1-3 : angle 1.24003 ( 3) hydrogen bonds : bond 0.04123 ( 501) hydrogen bonds : angle 4.70703 ( 1305) SS BOND : bond 0.00321 ( 36) SS BOND : angle 1.07175 ( 72) covalent geometry : bond 0.00364 (20188) covalent geometry : angle 0.61966 (27501) Misc. bond : bond 0.00084 ( 1) *********************** 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 259 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7602 (pt0) cc_final: 0.6952 (pt0) REVERT: A 178 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7483 (tpt170) REVERT: B 653 GLN cc_start: 0.7991 (mt0) cc_final: 0.7733 (mt0) REVERT: B 655 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7758 (mttp) REVERT: C 75 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7549 (ttm170) REVERT: G 164 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6366 (pp20) REVERT: G 173 TYR cc_start: 0.9230 (p90) cc_final: 0.8995 (p90) REVERT: G 445 CYS cc_start: 0.7510 (m) cc_final: 0.7177 (m) REVERT: I 661 LEU cc_start: 0.7463 (mm) cc_final: 0.7018 (tt) REVERT: R 104 ARG cc_start: 0.9113 (ttm170) cc_final: 0.8472 (ttm170) REVERT: S 3 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6914 (pp30) REVERT: S 109 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8757 (p0) outliers start: 61 outliers final: 50 residues processed: 237 average time/residue: 0.3033 time to fit residues: 112.6737 Evaluate side-chains 249 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 426 MET 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 128 THR Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 202 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 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 71 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 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 J residue 657 GLU Chi-restraints excluded: chain R residue 2 VAL 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 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 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 15 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 223 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.162527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125807 restraints weight = 24491.831| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.39 r_work: 0.3215 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20281 Z= 0.117 Angle : 0.632 17.574 27741 Z= 0.295 Chirality : 0.049 0.738 3287 Planarity : 0.004 0.074 3424 Dihedral : 6.982 80.943 3825 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Rotamer: Outliers : 2.65 % Allowed : 15.12 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2428 helix: 0.55 (0.28), residues: 388 sheet: 0.07 (0.18), residues: 812 loop : -1.02 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 103 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.001 PHE C 108 TYR 0.016 0.001 TYR A 173 ARG 0.005 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 38) link_NAG-ASN : angle 3.24585 ( 114) link_BETA1-4 : bond 0.00428 ( 17) link_BETA1-4 : angle 2.03566 ( 51) link_ALPHA1-3 : bond 0.01285 ( 1) link_ALPHA1-3 : angle 1.35459 ( 3) hydrogen bonds : bond 0.03647 ( 501) hydrogen bonds : angle 4.55534 ( 1305) SS BOND : bond 0.00318 ( 36) SS BOND : angle 0.97190 ( 72) covalent geometry : bond 0.00278 (20188) covalent geometry : angle 0.59031 (27501) Misc. bond : bond 0.00075 ( 1) *********************** 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 248 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7547 (pt0) cc_final: 0.6898 (pt0) REVERT: A 178 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7523 (tpt170) REVERT: B 645 LEU cc_start: 0.8057 (tp) cc_final: 0.7849 (tt) REVERT: B 653 GLN cc_start: 0.8017 (mt0) cc_final: 0.7754 (mt0) REVERT: B 655 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7772 (mttp) REVERT: C 75 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7708 (mtm180) REVERT: G 164 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6388 (pp20) REVERT: G 173 TYR cc_start: 0.9219 (p90) cc_final: 0.9009 (p90) REVERT: S 3 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6955 (pp30) REVERT: S 109 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8732 (p0) outliers start: 53 outliers final: 47 residues processed: 228 average time/residue: 0.3093 time to fit residues: 109.9908 Evaluate side-chains 243 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 MET 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 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 68 VAL Chi-restraints excluded: chain G residue 71 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 234 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 222 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 overall best weight: 1.0522 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.162026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125796 restraints weight = 24638.516| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.41 r_work: 0.3204 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20281 Z= 0.129 Angle : 0.640 17.601 27741 Z= 0.300 Chirality : 0.049 0.763 3287 Planarity : 0.004 0.073 3424 Dihedral : 6.934 79.651 3825 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.51 % Rotamer: Outliers : 2.70 % Allowed : 15.07 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2428 helix: 0.53 (0.28), residues: 387 sheet: 0.07 (0.18), residues: 812 loop : -1.03 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 103 HIS 0.003 0.001 HIS A 249 PHE 0.012 0.001 PHE C 108 TYR 0.017 0.001 TYR A 173 ARG 0.004 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 38) link_NAG-ASN : angle 3.25106 ( 114) link_BETA1-4 : bond 0.00404 ( 17) link_BETA1-4 : angle 2.06055 ( 51) link_ALPHA1-3 : bond 0.01196 ( 1) link_ALPHA1-3 : angle 1.39579 ( 3) hydrogen bonds : bond 0.03796 ( 501) hydrogen bonds : angle 4.57011 ( 1305) SS BOND : bond 0.00313 ( 36) SS BOND : angle 1.00244 ( 72) covalent geometry : bond 0.00312 (20188) covalent geometry : angle 0.59903 (27501) Misc. bond : bond 0.00083 ( 1) ********************** 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 248 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7550 (pt0) cc_final: 0.6898 (pt0) REVERT: A 178 ARG cc_start: 0.7854 (ttp-170) cc_final: 0.7535 (tpt170) REVERT: B 535 MET cc_start: 0.7912 (mtp) cc_final: 0.7518 (mmp) REVERT: B 542 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7349 (mtt180) REVERT: B 645 LEU cc_start: 0.8070 (tp) cc_final: 0.7860 (tt) REVERT: B 653 GLN cc_start: 0.7996 (mt0) cc_final: 0.7732 (mt0) REVERT: B 655 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7767 (mttp) REVERT: C 75 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7699 (mtm180) REVERT: C 104 ARG cc_start: 0.7121 (ptm160) cc_final: 0.6866 (ptm-80) REVERT: G 164 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6419 (pp20) REVERT: G 173 TYR cc_start: 0.9225 (p90) cc_final: 0.8951 (p90) REVERT: G 445 CYS cc_start: 0.7523 (m) cc_final: 0.7190 (m) REVERT: I 661 LEU cc_start: 0.7460 (mm) cc_final: 0.7071 (tt) REVERT: S 3 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6972 (pp30) REVERT: S 109 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8742 (p0) outliers start: 54 outliers final: 49 residues processed: 228 average time/residue: 0.2966 time to fit residues: 105.0853 Evaluate side-chains 243 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 MET 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 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 68 VAL Chi-restraints excluded: chain G residue 71 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 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 87 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 152 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124372 restraints weight = 24831.572| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.45 r_work: 0.3181 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20281 Z= 0.155 Angle : 0.665 18.225 27741 Z= 0.313 Chirality : 0.050 0.814 3287 Planarity : 0.004 0.073 3424 Dihedral : 7.009 77.871 3825 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.14 % Rotamer: Outliers : 2.90 % Allowed : 15.07 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2428 helix: 0.48 (0.28), residues: 385 sheet: 0.03 (0.18), residues: 803 loop : -1.10 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 103 HIS 0.004 0.001 HIS F 374 PHE 0.013 0.001 PHE G 383 TYR 0.017 0.001 TYR A 173 ARG 0.004 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 38) link_NAG-ASN : angle 3.33859 ( 114) link_BETA1-4 : bond 0.00399 ( 17) link_BETA1-4 : angle 2.11820 ( 51) link_ALPHA1-3 : bond 0.01147 ( 1) link_ALPHA1-3 : angle 1.37711 ( 3) hydrogen bonds : bond 0.04166 ( 501) hydrogen bonds : angle 4.65797 ( 1305) SS BOND : bond 0.00345 ( 36) SS BOND : angle 1.10294 ( 72) covalent geometry : bond 0.00380 (20188) covalent geometry : angle 0.62306 (27501) Misc. bond : bond 0.00094 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13116.93 seconds wall clock time: 233 minutes 3.19 seconds (13983.19 seconds total)