Starting phenix.real_space_refine on Sun Aug 24 12:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ult_42365/08_2025/8ult_42365.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 114 5.16 5 C 12422 2.51 5 N 3364 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19757 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3464 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1010 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1010 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1010 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 791 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" 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: "K" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "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: "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: "C" 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: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.79, per 1000 atoms: 0.19 Number of scatterers: 19757 At special positions: 0 Unit cell: (144.768, 137.28, 116.48, 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 114 16.00 O 3857 8.00 N 3364 7.00 C 12422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 234 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 234 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 392 " " NAG G 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 295 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 276 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 363 " " NAG b 1 " - " ASN E 386 " " NAG c 1 " - " ASN E 448 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 276 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 600.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.3% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.485A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.599A pdb=" N ARG A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) 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 425 through 429 removed outlier: 4.158A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.649A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.696A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.385A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.536A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.426A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.541A pdb=" N ARG C 151 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.855A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.712A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 removed outlier: 3.694A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.255A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.749A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 634 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.512A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.821A pdb=" N ARG E 151 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.964A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.862A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 481 removed outlier: 3.687A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.603A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.380A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.780A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 634 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.909A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.930A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.951A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.313A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.603A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.948A 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 94 removed outlier: 3.919A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.956A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.197A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.702A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.591A pdb=" N GLN A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.641A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.586A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.940A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.709A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.962A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.117A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.376A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.534A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.362A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.534A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.376A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.553A pdb=" N GLN C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.428A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.566A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.027A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.761A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.998A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 3.845A pdb=" N TYR E 435 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.307A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.722A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 359 " --> pdb=" O TRP E 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.575A pdb=" N GLN E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.509A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.830A pdb=" N SER H 102 " --> pdb=" O TRP H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.820A pdb=" N ALA H 35B" --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.552A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.906A pdb=" N SER I 102 " --> pdb=" O TRP I 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.537A pdb=" N ARG I 32 " --> pdb=" O ALA I 35B" (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA I 35B" --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.571A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.909A pdb=" N SER J 102 " --> pdb=" O TRP J 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.767A pdb=" N ALA J 35B" --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.027A pdb=" N HIS L 37 " --> pdb=" O ASN L 46 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASN L 46 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 13 removed outlier: 5.677A pdb=" N HIS M 37 " --> pdb=" O ASN M 46 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN M 46 " --> pdb=" O HIS M 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.370A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 803 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.24 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: 6295 1.35 - 1.48: 5226 1.48 - 1.61: 8503 1.61 - 1.75: 0 1.75 - 1.88: 150 Bond restraints: 20174 Sorted by residual: bond pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.09e-02 8.42e+03 9.70e+00 bond pdb=" N VAL C 36 " pdb=" CA VAL C 36 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N GLY E 354 " pdb=" CA GLY E 354 " ideal model delta sigma weight residual 1.447 1.477 -0.030 1.08e-02 8.57e+03 7.70e+00 bond pdb=" N CYS D 605 " pdb=" CA CYS D 605 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.62e+00 bond pdb=" N HIS L 37 " pdb=" CA HIS L 37 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.52e+00 ... (remaining 20169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 26646 1.98 - 3.95: 733 3.95 - 5.93: 50 5.93 - 7.90: 9 7.90 - 9.88: 4 Bond angle restraints: 27442 Sorted by residual: angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 124.28 -9.88 2.30e+00 1.89e-01 1.84e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 123.77 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" C ARG L 66 " pdb=" CA ARG L 66 " pdb=" CB ARG L 66 " ideal model delta sigma weight residual 110.14 103.88 6.26 1.60e+00 3.91e-01 1.53e+01 angle pdb=" CA THR L 50 " pdb=" CB THR L 50 " pdb=" OG1 THR L 50 " ideal model delta sigma weight residual 109.60 103.87 5.73 1.50e+00 4.44e-01 1.46e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 111.88 108.11 3.77 1.06e+00 8.90e-01 1.27e+01 ... (remaining 27437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 12037 21.90 - 43.80: 726 43.80 - 65.69: 126 65.69 - 87.59: 32 87.59 - 109.49: 12 Dihedral angle restraints: 12933 sinusoidal: 5997 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " pdb=" SG CYS E 331 " pdb=" CB CYS E 331 " ideal model delta sinusoidal sigma weight residual 93.00 37.88 55.12 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -138.09 52.09 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -36.48 -49.52 1 1.00e+01 1.00e-02 3.37e+01 ... (remaining 12930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2964 0.089 - 0.177: 313 0.177 - 0.266: 11 0.266 - 0.355: 4 0.355 - 0.444: 1 Chirality restraints: 3293 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 9.75e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 276 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C1 NAG E 606 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 606 " pdb=" O5 NAG E 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 3290 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 1 " -0.119 2.00e-02 2.50e+03 9.98e-02 1.25e+02 pdb=" C7 NAG e 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG e 1 " -0.087 2.00e-02 2.50e+03 pdb=" N2 NAG e 1 " 0.165 2.00e-02 2.50e+03 pdb=" O7 NAG e 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " -0.115 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" C7 NAG e 2 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " 0.156 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 500 " -0.440 9.50e-02 1.11e+02 1.97e-01 2.39e+01 pdb=" NE ARG C 500 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 500 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 500 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 500 " -0.015 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 958 2.72 - 3.27: 19685 3.27 - 3.81: 32400 3.81 - 4.36: 38258 4.36 - 4.90: 66134 Nonbonded interactions: 157435 Sorted by model distance: nonbonded pdb=" OG1 THR F 627 " pdb=" OE1 GLN F 630 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP E 113 " pdb=" NH1 ARG E 429 " model vdw 2.181 3.120 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 173 " pdb=" OD1 ASP A 321A" model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN F 611 " pdb=" OG SER F 613 " model vdw 2.221 3.040 ... (remaining 157430 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 33 through 609) selection = (chain 'C' and resid 33 through 609) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'S' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.005 0.071 20283 Z= 0.270 Angle : 0.734 10.855 27730 Z= 0.388 Chirality : 0.050 0.444 3293 Planarity : 0.007 0.197 3412 Dihedral : 14.074 109.488 8340 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.17), residues: 2358 helix: 1.09 (0.27), residues: 426 sheet: 0.00 (0.19), residues: 756 loop : -0.39 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 151 TYR 0.030 0.002 TYR L 49 PHE 0.009 0.001 PHE L 71 TRP 0.020 0.002 TRP C 479 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00503 (20174) covalent geometry : angle 0.69980 (27442) SS BOND : bond 0.00538 ( 39) SS BOND : angle 1.57562 ( 78) hydrogen bonds : bond 0.20201 ( 744) hydrogen bonds : angle 8.76275 ( 2106) link_BETA1-4 : bond 0.01138 ( 22) link_BETA1-4 : angle 2.38900 ( 66) link_NAG-ASN : bond 0.00474 ( 48) link_NAG-ASN : angle 2.55393 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 ILE cc_start: 0.9092 (mt) cc_final: 0.8790 (tt) REVERT: B 625 ASN cc_start: 0.8143 (t0) cc_final: 0.7900 (t0) REVERT: B 646 LEU cc_start: 0.9642 (mt) cc_final: 0.9434 (mt) REVERT: C 475 MET cc_start: 0.8919 (mmm) cc_final: 0.8507 (mmt) REVERT: D 536 THR cc_start: 0.9326 (p) cc_final: 0.8833 (p) REVERT: D 586 TYR cc_start: 0.9129 (t80) cc_final: 0.8875 (t80) REVERT: D 625 ASN cc_start: 0.8145 (t0) cc_final: 0.7768 (t0) REVERT: E 475 MET cc_start: 0.8933 (mmm) cc_final: 0.8480 (mmt) REVERT: F 536 THR cc_start: 0.9258 (p) cc_final: 0.8808 (p) REVERT: F 540 GLN cc_start: 0.8999 (mp10) cc_final: 0.8738 (mp10) REVERT: F 625 ASN cc_start: 0.8210 (t0) cc_final: 0.7980 (t0) REVERT: F 658 GLN cc_start: 0.9059 (tt0) cc_final: 0.8767 (tt0) REVERT: H 72 ASP cc_start: 0.8548 (t0) cc_final: 0.8092 (t0) REVERT: I 59 TYR cc_start: 0.8181 (m-10) cc_final: 0.7659 (m-80) REVERT: I 72 ASP cc_start: 0.8475 (t0) cc_final: 0.8063 (t0) REVERT: J 59 TYR cc_start: 0.7952 (m-80) cc_final: 0.7630 (m-10) REVERT: J 72 ASP cc_start: 0.8583 (t0) cc_final: 0.8162 (t0) REVERT: J 89 THR cc_start: 0.8995 (p) cc_final: 0.8434 (p) REVERT: J 91 TYR cc_start: 0.9095 (m-80) cc_final: 0.8755 (m-80) REVERT: J 107 THR cc_start: 0.9206 (m) cc_final: 0.8774 (m) REVERT: L 35 TRP cc_start: 0.9212 (m100) cc_final: 0.8938 (m100) REVERT: L 36 TYR cc_start: 0.8468 (m-80) cc_final: 0.8101 (m-10) REVERT: M 47 LEU cc_start: 0.9252 (tt) cc_final: 0.9044 (tt) REVERT: M 82 ASP cc_start: 0.7958 (m-30) cc_final: 0.7730 (m-30) REVERT: M 103 THR cc_start: 0.9326 (p) cc_final: 0.9107 (p) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.1140 time to fit residues: 87.4042 Evaluate side-chains 369 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 652 GLN B 656 ASN C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35IASN I 6 GLN I 35IASN I 97 ASN J 6 GLN J 39 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.071963 restraints weight = 55137.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.074366 restraints weight = 25102.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076020 restraints weight = 15033.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077243 restraints weight = 10493.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078012 restraints weight = 7936.126| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20283 Z= 0.144 Angle : 0.643 10.994 27730 Z= 0.321 Chirality : 0.046 0.244 3293 Planarity : 0.004 0.041 3412 Dihedral : 9.077 71.408 4044 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.70 % Allowed : 10.50 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.18), residues: 2358 helix: 1.15 (0.26), residues: 447 sheet: 0.29 (0.18), residues: 807 loop : -0.39 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 429 TYR 0.019 0.002 TYR L 70 PHE 0.022 0.001 PHE A 233 TRP 0.021 0.001 TRP B 610 HIS 0.009 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00321 (20174) covalent geometry : angle 0.60843 (27442) SS BOND : bond 0.00464 ( 39) SS BOND : angle 1.25529 ( 78) hydrogen bonds : bond 0.04408 ( 744) hydrogen bonds : angle 6.07286 ( 2106) link_BETA1-4 : bond 0.00480 ( 22) link_BETA1-4 : angle 1.92482 ( 66) link_NAG-ASN : bond 0.00471 ( 48) link_NAG-ASN : angle 2.55702 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 425 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9415 (mt) cc_final: 0.9204 (mt) REVERT: A 484 TYR cc_start: 0.9163 (p90) cc_final: 0.8721 (p90) REVERT: B 535 MET cc_start: 0.9264 (mmm) cc_final: 0.9036 (mmm) REVERT: B 540 GLN cc_start: 0.8842 (mp10) cc_final: 0.8632 (mp10) REVERT: B 586 TYR cc_start: 0.9502 (t80) cc_final: 0.9220 (t80) REVERT: B 591 GLN cc_start: 0.9040 (tp40) cc_final: 0.8686 (tp40) REVERT: B 621 GLU cc_start: 0.8692 (tp30) cc_final: 0.8355 (tp30) REVERT: B 625 ASN cc_start: 0.8163 (t0) cc_final: 0.7913 (t0) REVERT: B 650 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 466 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7462 (mt-10) REVERT: D 621 GLU cc_start: 0.8750 (tp30) cc_final: 0.8506 (tp30) REVERT: D 654 GLU cc_start: 0.8637 (tt0) cc_final: 0.8426 (tt0) REVERT: E 271 MET cc_start: 0.7800 (mtp) cc_final: 0.7502 (mtp) REVERT: E 475 MET cc_start: 0.8956 (mmm) cc_final: 0.8709 (mmt) REVERT: F 536 THR cc_start: 0.9233 (p) cc_final: 0.8732 (p) REVERT: F 540 GLN cc_start: 0.8929 (mp10) cc_final: 0.8656 (mp10) REVERT: F 621 GLU cc_start: 0.8786 (tp30) cc_final: 0.8565 (tp30) REVERT: H 59 TYR cc_start: 0.8341 (m-10) cc_final: 0.8098 (m-10) REVERT: H 79 TYR cc_start: 0.9327 (m-80) cc_final: 0.9073 (m-10) REVERT: I 31 TYR cc_start: 0.8955 (t80) cc_final: 0.8732 (t80) REVERT: I 100 ARG cc_start: 0.8285 (ttt180) cc_final: 0.7777 (ttt180) REVERT: J 89 THR cc_start: 0.8855 (p) cc_final: 0.8381 (t) REVERT: J 91 TYR cc_start: 0.9090 (m-80) cc_final: 0.8501 (m-80) REVERT: L 35 TRP cc_start: 0.9340 (m100) cc_final: 0.9071 (m100) REVERT: L 36 TYR cc_start: 0.8202 (m-80) cc_final: 0.7822 (m-80) REVERT: M 49 TYR cc_start: 0.8480 (p90) cc_final: 0.7292 (p90) REVERT: N 81 GLU cc_start: 0.8328 (pm20) cc_final: 0.8026 (pm20) outliers start: 35 outliers final: 23 residues processed: 434 average time/residue: 0.1133 time to fit residues: 79.6907 Evaluate side-chains 384 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN H 6 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.068426 restraints weight = 56357.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070811 restraints weight = 26061.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072433 restraints weight = 15649.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073632 restraints weight = 10987.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.074372 restraints weight = 8406.798| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20283 Z= 0.243 Angle : 0.690 11.150 27730 Z= 0.341 Chirality : 0.048 0.290 3293 Planarity : 0.004 0.049 3412 Dihedral : 7.758 59.424 4044 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2358 helix: 1.21 (0.26), residues: 438 sheet: 0.38 (0.18), residues: 777 loop : -0.47 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100D TYR 0.020 0.002 TYR J 59 PHE 0.014 0.002 PHE A 233 TRP 0.027 0.002 TRP D 610 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00551 (20174) covalent geometry : angle 0.65274 (27442) SS BOND : bond 0.00521 ( 39) SS BOND : angle 1.57291 ( 78) hydrogen bonds : bond 0.04239 ( 744) hydrogen bonds : angle 5.59222 ( 2106) link_BETA1-4 : bond 0.00333 ( 22) link_BETA1-4 : angle 2.06397 ( 66) link_NAG-ASN : bond 0.00526 ( 48) link_NAG-ASN : angle 2.70248 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 372 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8547 (p) REVERT: B 586 TYR cc_start: 0.9568 (t80) cc_final: 0.9233 (t80) REVERT: B 591 GLN cc_start: 0.9111 (tp40) cc_final: 0.8627 (tp40) REVERT: B 621 GLU cc_start: 0.8766 (tp30) cc_final: 0.8458 (tp30) REVERT: B 625 ASN cc_start: 0.8206 (t0) cc_final: 0.7864 (t0) REVERT: B 650 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8785 (tm-30) REVERT: D 540 GLN cc_start: 0.8770 (mp10) cc_final: 0.8508 (mp10) REVERT: D 586 TYR cc_start: 0.9535 (t80) cc_final: 0.8963 (t80) REVERT: D 606 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9186 (p) REVERT: D 625 ASN cc_start: 0.7981 (t0) cc_final: 0.7763 (t0) REVERT: E 271 MET cc_start: 0.7852 (mtp) cc_final: 0.7649 (mtp) REVERT: F 536 THR cc_start: 0.9280 (p) cc_final: 0.8736 (p) REVERT: F 540 GLN cc_start: 0.8877 (mp10) cc_final: 0.8528 (mp10) REVERT: F 625 ASN cc_start: 0.8028 (t0) cc_final: 0.7776 (t0) REVERT: H 6 GLN cc_start: 0.8362 (mt0) cc_final: 0.8134 (tt0) REVERT: J 59 TYR cc_start: 0.8185 (m-10) cc_final: 0.7894 (m-80) REVERT: J 100 ARG cc_start: 0.8352 (ttt180) cc_final: 0.8113 (ttt180) REVERT: M 49 TYR cc_start: 0.8612 (p90) cc_final: 0.7756 (p90) REVERT: N 49 TYR cc_start: 0.8558 (p90) cc_final: 0.7955 (p90) REVERT: N 81 GLU cc_start: 0.8354 (pm20) cc_final: 0.8095 (pm20) REVERT: N 89 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8777 (tt0) outliers start: 59 outliers final: 43 residues processed: 406 average time/residue: 0.1093 time to fit residues: 72.4566 Evaluate side-chains 386 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 118 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 6 GLN L 37 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.066309 restraints weight = 56493.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068702 restraints weight = 26335.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070359 restraints weight = 15931.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071422 restraints weight = 11207.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072195 restraints weight = 8720.758| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20283 Z= 0.225 Angle : 0.673 11.057 27730 Z= 0.331 Chirality : 0.047 0.305 3293 Planarity : 0.004 0.040 3412 Dihedral : 7.041 59.802 4044 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.40 % Allowed : 14.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2358 helix: 1.30 (0.26), residues: 435 sheet: 0.40 (0.18), residues: 765 loop : -0.45 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 100D TYR 0.041 0.002 TYR L 49 PHE 0.018 0.002 PHE A 53 TRP 0.027 0.002 TRP B 571 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00508 (20174) covalent geometry : angle 0.63600 (27442) SS BOND : bond 0.00482 ( 39) SS BOND : angle 1.69796 ( 78) hydrogen bonds : bond 0.03896 ( 744) hydrogen bonds : angle 5.33886 ( 2106) link_BETA1-4 : bond 0.00344 ( 22) link_BETA1-4 : angle 1.87633 ( 66) link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 2.63158 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 383 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 586 TYR cc_start: 0.9555 (t80) cc_final: 0.9200 (t80) REVERT: B 591 GLN cc_start: 0.9113 (tp40) cc_final: 0.8660 (tp40) REVERT: B 621 GLU cc_start: 0.8734 (tp30) cc_final: 0.8430 (tp30) REVERT: B 625 ASN cc_start: 0.8183 (t0) cc_final: 0.7826 (t0) REVERT: B 650 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 540 GLN cc_start: 0.8745 (mp10) cc_final: 0.8472 (mp10) REVERT: D 586 TYR cc_start: 0.9544 (t80) cc_final: 0.9019 (t80) REVERT: D 650 GLN cc_start: 0.9476 (tp40) cc_final: 0.8655 (tm-30) REVERT: D 654 GLU cc_start: 0.8610 (tt0) cc_final: 0.8339 (tt0) REVERT: E 217 TYR cc_start: 0.8110 (m-80) cc_final: 0.7739 (m-80) REVERT: E 323 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9091 (mp) REVERT: F 536 THR cc_start: 0.9299 (p) cc_final: 0.8758 (p) REVERT: F 540 GLN cc_start: 0.8889 (mp10) cc_final: 0.8515 (mp10) REVERT: F 625 ASN cc_start: 0.7944 (t0) cc_final: 0.7608 (t0) REVERT: M 49 TYR cc_start: 0.8649 (p90) cc_final: 0.7880 (p90) REVERT: N 49 TYR cc_start: 0.8561 (p90) cc_final: 0.8027 (p90) REVERT: N 82 ASP cc_start: 0.8269 (m-30) cc_final: 0.7999 (m-30) REVERT: N 89 GLN cc_start: 0.9156 (tt0) cc_final: 0.8729 (tt0) outliers start: 70 outliers final: 53 residues processed: 428 average time/residue: 0.1083 time to fit residues: 76.5332 Evaluate side-chains 400 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 345 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 98 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 348 GLN C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** L 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.067010 restraints weight = 56392.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069404 restraints weight = 26594.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071070 restraints weight = 16182.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072140 restraints weight = 11392.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072918 restraints weight = 8875.638| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20283 Z= 0.180 Angle : 0.646 11.041 27730 Z= 0.319 Chirality : 0.046 0.289 3293 Planarity : 0.003 0.041 3412 Dihedral : 6.641 59.882 4044 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.55 % Allowed : 15.99 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2358 helix: 1.35 (0.27), residues: 435 sheet: 0.39 (0.18), residues: 768 loop : -0.39 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 476 TYR 0.034 0.002 TYR L 49 PHE 0.016 0.001 PHE A 53 TRP 0.036 0.002 TRP B 571 HIS 0.020 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00410 (20174) covalent geometry : angle 0.61098 (27442) SS BOND : bond 0.00455 ( 39) SS BOND : angle 1.61234 ( 78) hydrogen bonds : bond 0.03729 ( 744) hydrogen bonds : angle 5.16692 ( 2106) link_BETA1-4 : bond 0.00362 ( 22) link_BETA1-4 : angle 1.75019 ( 66) link_NAG-ASN : bond 0.00424 ( 48) link_NAG-ASN : angle 2.53884 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 371 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8522 (p) REVERT: B 586 TYR cc_start: 0.9543 (t80) cc_final: 0.9166 (t80) REVERT: B 591 GLN cc_start: 0.9093 (tp40) cc_final: 0.8693 (tp40) REVERT: B 621 GLU cc_start: 0.8743 (tp30) cc_final: 0.8481 (tp30) REVERT: B 625 ASN cc_start: 0.8156 (t0) cc_final: 0.7762 (t0) REVERT: B 650 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8733 (tm-30) REVERT: D 540 GLN cc_start: 0.8709 (mp10) cc_final: 0.8415 (mp10) REVERT: D 586 TYR cc_start: 0.9533 (t80) cc_final: 0.9083 (t80) REVERT: D 625 ASN cc_start: 0.8024 (t0) cc_final: 0.7693 (t0) REVERT: D 650 GLN cc_start: 0.9453 (tp40) cc_final: 0.8692 (tm-30) REVERT: D 654 GLU cc_start: 0.8624 (tt0) cc_final: 0.8297 (tt0) REVERT: E 217 TYR cc_start: 0.8126 (m-80) cc_final: 0.7777 (m-10) REVERT: E 475 MET cc_start: 0.9148 (mmt) cc_final: 0.8920 (mmm) REVERT: F 536 THR cc_start: 0.9316 (p) cc_final: 0.8789 (p) REVERT: F 540 GLN cc_start: 0.8883 (mp10) cc_final: 0.8527 (mp10) REVERT: F 625 ASN cc_start: 0.7987 (t0) cc_final: 0.7571 (t0) REVERT: H 6 GLN cc_start: 0.8314 (tt0) cc_final: 0.7962 (tt0) REVERT: H 107 THR cc_start: 0.9444 (m) cc_final: 0.9063 (m) REVERT: I 72 ASP cc_start: 0.8348 (t0) cc_final: 0.7953 (t0) REVERT: J 59 TYR cc_start: 0.8176 (m-10) cc_final: 0.7959 (m-80) REVERT: L 37 HIS cc_start: 0.7900 (t-170) cc_final: 0.7553 (t70) REVERT: L 86 TYR cc_start: 0.8881 (m-80) cc_final: 0.8362 (m-10) REVERT: L 96 ASP cc_start: 0.9184 (p0) cc_final: 0.8969 (p0) REVERT: M 49 TYR cc_start: 0.8633 (p90) cc_final: 0.7903 (p90) REVERT: N 36 TYR cc_start: 0.8946 (m-80) cc_final: 0.8698 (m-10) REVERT: N 49 TYR cc_start: 0.8570 (p90) cc_final: 0.8065 (p90) outliers start: 73 outliers final: 55 residues processed: 414 average time/residue: 0.1069 time to fit residues: 72.9073 Evaluate side-chains 408 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 153 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN L 37 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067789 restraints weight = 55780.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.070208 restraints weight = 25989.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071767 restraints weight = 15687.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072956 restraints weight = 11213.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073704 restraints weight = 8549.523| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20283 Z= 0.149 Angle : 0.636 11.013 27730 Z= 0.312 Chirality : 0.046 0.281 3293 Planarity : 0.003 0.046 3412 Dihedral : 6.322 59.141 4044 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.87 % Allowed : 17.20 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2358 helix: 1.44 (0.27), residues: 432 sheet: 0.42 (0.18), residues: 768 loop : -0.35 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.033 0.002 TYR L 49 PHE 0.017 0.001 PHE F 519 TRP 0.041 0.001 TRP D 571 HIS 0.010 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00340 (20174) covalent geometry : angle 0.60283 (27442) SS BOND : bond 0.00442 ( 39) SS BOND : angle 1.54949 ( 78) hydrogen bonds : bond 0.03529 ( 744) hydrogen bonds : angle 5.03316 ( 2106) link_BETA1-4 : bond 0.00365 ( 22) link_BETA1-4 : angle 1.66015 ( 66) link_NAG-ASN : bond 0.00396 ( 48) link_NAG-ASN : angle 2.44545 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8471 (p) REVERT: B 586 TYR cc_start: 0.9531 (t80) cc_final: 0.9185 (t80) REVERT: B 591 GLN cc_start: 0.9087 (tp40) cc_final: 0.8716 (tp40) REVERT: B 621 GLU cc_start: 0.8774 (tp30) cc_final: 0.8518 (tp30) REVERT: B 625 ASN cc_start: 0.8137 (t0) cc_final: 0.7769 (t0) REVERT: B 647 GLU cc_start: 0.8873 (tt0) cc_final: 0.8651 (tt0) REVERT: B 650 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8685 (tm-30) REVERT: D 537 LEU cc_start: 0.9390 (mt) cc_final: 0.9114 (mt) REVERT: D 540 GLN cc_start: 0.8581 (mp10) cc_final: 0.8295 (mp10) REVERT: D 586 TYR cc_start: 0.9519 (t80) cc_final: 0.9110 (t80) REVERT: D 625 ASN cc_start: 0.7946 (t0) cc_final: 0.7670 (t0) REVERT: D 650 GLN cc_start: 0.9455 (tp40) cc_final: 0.8741 (tm-30) REVERT: D 654 GLU cc_start: 0.8615 (tt0) cc_final: 0.8271 (tt0) REVERT: E 217 TYR cc_start: 0.8087 (m-80) cc_final: 0.7745 (m-10) REVERT: F 536 THR cc_start: 0.9302 (p) cc_final: 0.8761 (p) REVERT: F 540 GLN cc_start: 0.8869 (mp10) cc_final: 0.8520 (mp10) REVERT: F 625 ASN cc_start: 0.7892 (t0) cc_final: 0.7527 (t0) REVERT: L 37 HIS cc_start: 0.7717 (t-90) cc_final: 0.7468 (t70) REVERT: L 86 TYR cc_start: 0.8945 (m-80) cc_final: 0.8356 (m-10) REVERT: L 96 ASP cc_start: 0.9170 (p0) cc_final: 0.8965 (p0) REVERT: M 49 TYR cc_start: 0.8634 (p90) cc_final: 0.7894 (p90) REVERT: N 27 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7722 (tm-30) REVERT: N 37 HIS cc_start: 0.8351 (t-170) cc_final: 0.8096 (t70) REVERT: N 49 TYR cc_start: 0.8529 (p90) cc_final: 0.8137 (p90) REVERT: N 81 GLU cc_start: 0.8408 (pm20) cc_final: 0.8158 (pm20) REVERT: N 89 GLN cc_start: 0.9063 (tt0) cc_final: 0.8845 (tt0) outliers start: 59 outliers final: 48 residues processed: 418 average time/residue: 0.1080 time to fit residues: 74.1003 Evaluate side-chains 411 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 0.0020 chunk 199 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 543 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068630 restraints weight = 56212.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071076 restraints weight = 26021.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072786 restraints weight = 15601.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073866 restraints weight = 10853.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074687 restraints weight = 8369.318| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20283 Z= 0.128 Angle : 0.633 11.545 27730 Z= 0.309 Chirality : 0.045 0.274 3293 Planarity : 0.003 0.042 3412 Dihedral : 6.005 57.917 4044 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.92 % Allowed : 18.08 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.18), residues: 2358 helix: 1.31 (0.27), residues: 444 sheet: 0.45 (0.18), residues: 768 loop : -0.30 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 476 TYR 0.033 0.002 TYR L 49 PHE 0.009 0.001 PHE A 53 TRP 0.044 0.002 TRP F 571 HIS 0.006 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00294 (20174) covalent geometry : angle 0.60292 (27442) SS BOND : bond 0.00431 ( 39) SS BOND : angle 1.52700 ( 78) hydrogen bonds : bond 0.03365 ( 744) hydrogen bonds : angle 4.91787 ( 2106) link_BETA1-4 : bond 0.00385 ( 22) link_BETA1-4 : angle 1.59865 ( 66) link_NAG-ASN : bond 0.00380 ( 48) link_NAG-ASN : angle 2.35400 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 393 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 479 TRP cc_start: 0.8568 (m-10) cc_final: 0.8256 (m-90) REVERT: B 586 TYR cc_start: 0.9517 (t80) cc_final: 0.9138 (t80) REVERT: B 591 GLN cc_start: 0.9055 (tp40) cc_final: 0.8668 (tp40) REVERT: B 621 GLU cc_start: 0.8750 (tp30) cc_final: 0.8511 (tp30) REVERT: B 625 ASN cc_start: 0.8091 (t0) cc_final: 0.7729 (t0) REVERT: B 650 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8680 (tm-30) REVERT: D 530 MET cc_start: 0.8564 (tpp) cc_final: 0.8342 (tpp) REVERT: D 537 LEU cc_start: 0.9382 (mt) cc_final: 0.9052 (mt) REVERT: D 540 GLN cc_start: 0.8596 (mp10) cc_final: 0.8323 (mp10) REVERT: D 586 TYR cc_start: 0.9504 (t80) cc_final: 0.9098 (t80) REVERT: D 625 ASN cc_start: 0.7951 (t0) cc_final: 0.7722 (t0) REVERT: D 650 GLN cc_start: 0.9439 (tp40) cc_final: 0.8766 (tm-30) REVERT: D 654 GLU cc_start: 0.8613 (tt0) cc_final: 0.8264 (tt0) REVERT: E 217 TYR cc_start: 0.8077 (m-80) cc_final: 0.7637 (m-10) REVERT: F 536 THR cc_start: 0.9281 (p) cc_final: 0.8739 (p) REVERT: F 540 GLN cc_start: 0.8856 (mp10) cc_final: 0.8510 (mp10) REVERT: F 625 ASN cc_start: 0.7942 (t0) cc_final: 0.7578 (t0) REVERT: L 35 TRP cc_start: 0.9262 (m100) cc_final: 0.8984 (m100) REVERT: L 86 TYR cc_start: 0.8968 (m-80) cc_final: 0.8417 (m-10) REVERT: M 49 TYR cc_start: 0.8614 (p90) cc_final: 0.7850 (p90) REVERT: N 49 TYR cc_start: 0.8486 (p90) cc_final: 0.8104 (p90) REVERT: N 81 GLU cc_start: 0.8405 (pm20) cc_final: 0.8161 (pm20) REVERT: N 89 GLN cc_start: 0.9095 (tt0) cc_final: 0.8892 (tt0) outliers start: 60 outliers final: 52 residues processed: 427 average time/residue: 0.1103 time to fit residues: 77.1249 Evaluate side-chains 418 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 150 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN C 195 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068635 restraints weight = 55733.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071054 restraints weight = 25990.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072635 restraints weight = 15641.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073817 restraints weight = 11125.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.074600 restraints weight = 8478.972| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20283 Z= 0.139 Angle : 0.641 11.783 27730 Z= 0.312 Chirality : 0.045 0.275 3293 Planarity : 0.003 0.041 3412 Dihedral : 5.879 57.423 4044 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 18.66 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2358 helix: 1.32 (0.27), residues: 444 sheet: 0.43 (0.18), residues: 771 loop : -0.25 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 42 TYR 0.032 0.002 TYR L 49 PHE 0.014 0.001 PHE B 519 TRP 0.034 0.001 TRP F 571 HIS 0.023 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00320 (20174) covalent geometry : angle 0.61196 (27442) SS BOND : bond 0.00437 ( 39) SS BOND : angle 1.49211 ( 78) hydrogen bonds : bond 0.03321 ( 744) hydrogen bonds : angle 4.85736 ( 2106) link_BETA1-4 : bond 0.00372 ( 22) link_BETA1-4 : angle 1.58906 ( 66) link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.34014 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 372 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 479 TRP cc_start: 0.8461 (m-10) cc_final: 0.8257 (m-90) REVERT: B 538 THR cc_start: 0.8755 (p) cc_final: 0.8521 (p) REVERT: B 586 TYR cc_start: 0.9513 (t80) cc_final: 0.9164 (t80) REVERT: B 591 GLN cc_start: 0.9068 (tp40) cc_final: 0.8670 (tp40) REVERT: B 621 GLU cc_start: 0.8770 (tp30) cc_final: 0.8531 (tp30) REVERT: B 625 ASN cc_start: 0.8113 (t0) cc_final: 0.7744 (t0) REVERT: D 537 LEU cc_start: 0.9368 (mt) cc_final: 0.9034 (mt) REVERT: D 540 GLN cc_start: 0.8603 (mp10) cc_final: 0.8327 (mp10) REVERT: D 586 TYR cc_start: 0.9501 (t80) cc_final: 0.9100 (t80) REVERT: D 650 GLN cc_start: 0.9460 (tp40) cc_final: 0.8780 (tm-30) REVERT: D 654 GLU cc_start: 0.8610 (tt0) cc_final: 0.8276 (tt0) REVERT: E 217 TYR cc_start: 0.8107 (m-80) cc_final: 0.7681 (m-10) REVERT: F 536 THR cc_start: 0.9275 (p) cc_final: 0.8728 (p) REVERT: F 540 GLN cc_start: 0.8874 (mp10) cc_final: 0.8525 (mp10) REVERT: F 625 ASN cc_start: 0.7889 (t0) cc_final: 0.7522 (t0) REVERT: L 35 TRP cc_start: 0.9244 (m100) cc_final: 0.9008 (m100) REVERT: M 49 TYR cc_start: 0.8640 (p90) cc_final: 0.7926 (p90) REVERT: N 49 TYR cc_start: 0.8484 (p90) cc_final: 0.8095 (p90) REVERT: N 81 GLU cc_start: 0.8387 (pm20) cc_final: 0.8163 (pm20) outliers start: 61 outliers final: 55 residues processed: 407 average time/residue: 0.1060 time to fit residues: 71.2383 Evaluate side-chains 414 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 182 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN C 136 ASN C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067783 restraints weight = 55696.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070192 restraints weight = 25530.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071825 restraints weight = 15144.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072993 restraints weight = 10516.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.073722 restraints weight = 8016.023| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20283 Z= 0.119 Angle : 0.639 11.616 27730 Z= 0.312 Chirality : 0.045 0.268 3293 Planarity : 0.003 0.039 3412 Dihedral : 5.679 57.716 4044 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.82 % Allowed : 19.24 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2358 helix: 1.33 (0.27), residues: 444 sheet: 0.47 (0.18), residues: 771 loop : -0.22 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.035 0.002 TYR L 49 PHE 0.008 0.001 PHE I 35D TRP 0.028 0.001 TRP C 479 HIS 0.018 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00272 (20174) covalent geometry : angle 0.61190 (27442) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.46806 ( 78) hydrogen bonds : bond 0.03203 ( 744) hydrogen bonds : angle 4.76549 ( 2106) link_BETA1-4 : bond 0.00389 ( 22) link_BETA1-4 : angle 1.50939 ( 66) link_NAG-ASN : bond 0.00369 ( 48) link_NAG-ASN : angle 2.23937 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 393 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8341 (p) REVERT: B 586 TYR cc_start: 0.9478 (t80) cc_final: 0.9070 (t80) REVERT: B 591 GLN cc_start: 0.9063 (tp40) cc_final: 0.8648 (tp40) REVERT: B 621 GLU cc_start: 0.8784 (tp30) cc_final: 0.8570 (tp30) REVERT: B 625 ASN cc_start: 0.8081 (t0) cc_final: 0.7785 (t0) REVERT: D 537 LEU cc_start: 0.9322 (mt) cc_final: 0.8985 (mt) REVERT: D 540 GLN cc_start: 0.8621 (mp10) cc_final: 0.8332 (mp10) REVERT: D 586 TYR cc_start: 0.9450 (t80) cc_final: 0.9033 (t80) REVERT: D 591 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 650 GLN cc_start: 0.9461 (tp40) cc_final: 0.8803 (tm-30) REVERT: D 654 GLU cc_start: 0.8649 (tt0) cc_final: 0.8313 (tt0) REVERT: E 217 TYR cc_start: 0.8032 (m-80) cc_final: 0.7675 (m-10) REVERT: F 536 THR cc_start: 0.9338 (p) cc_final: 0.8810 (p) REVERT: F 540 GLN cc_start: 0.8874 (mp10) cc_final: 0.8502 (mp10) REVERT: F 625 ASN cc_start: 0.7888 (t0) cc_final: 0.7633 (t0) REVERT: I 36 TRP cc_start: 0.9453 (m100) cc_final: 0.8679 (m100) REVERT: I 100 ARG cc_start: 0.8617 (ttt180) cc_final: 0.7879 (ttt180) REVERT: L 35 TRP cc_start: 0.9178 (m100) cc_final: 0.8880 (m100) REVERT: N 49 TYR cc_start: 0.8410 (p90) cc_final: 0.8071 (p90) REVERT: N 70 TYR cc_start: 0.8325 (t80) cc_final: 0.8115 (t80) REVERT: N 81 GLU cc_start: 0.8351 (pm20) cc_final: 0.8148 (pm20) REVERT: N 103 THR cc_start: 0.9098 (p) cc_final: 0.8403 (p) outliers start: 58 outliers final: 50 residues processed: 430 average time/residue: 0.1084 time to fit residues: 77.1085 Evaluate side-chains 416 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN C 195 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.067408 restraints weight = 56250.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069834 restraints weight = 25878.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071384 restraints weight = 15398.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072599 restraints weight = 10933.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073336 restraints weight = 8311.145| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20283 Z= 0.134 Angle : 0.660 13.453 27730 Z= 0.320 Chirality : 0.045 0.271 3293 Planarity : 0.003 0.040 3412 Dihedral : 5.644 57.116 4044 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.53 % Allowed : 20.02 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2358 helix: 1.30 (0.27), residues: 444 sheet: 0.46 (0.18), residues: 771 loop : -0.21 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.029 0.002 TYR L 49 PHE 0.015 0.001 PHE B 519 TRP 0.069 0.002 TRP M 35 HIS 0.017 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00312 (20174) covalent geometry : angle 0.63432 (27442) SS BOND : bond 0.00426 ( 39) SS BOND : angle 1.46205 ( 78) hydrogen bonds : bond 0.03218 ( 744) hydrogen bonds : angle 4.75846 ( 2106) link_BETA1-4 : bond 0.00366 ( 22) link_BETA1-4 : angle 1.51585 ( 66) link_NAG-ASN : bond 0.00350 ( 48) link_NAG-ASN : angle 2.25093 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 586 TYR cc_start: 0.9478 (t80) cc_final: 0.9072 (t80) REVERT: B 591 GLN cc_start: 0.9080 (tp40) cc_final: 0.8774 (tp40) REVERT: B 621 GLU cc_start: 0.8811 (tp30) cc_final: 0.8598 (tp30) REVERT: B 625 ASN cc_start: 0.8101 (t0) cc_final: 0.7792 (t0) REVERT: C 150 MET cc_start: 0.8285 (mmm) cc_final: 0.8025 (tpp) REVERT: D 537 LEU cc_start: 0.9270 (mt) cc_final: 0.8917 (mt) REVERT: D 540 GLN cc_start: 0.8610 (mp10) cc_final: 0.8305 (mp10) REVERT: D 586 TYR cc_start: 0.9430 (t80) cc_final: 0.9162 (t80) REVERT: D 650 GLN cc_start: 0.9483 (tp40) cc_final: 0.8801 (tm-30) REVERT: D 654 GLU cc_start: 0.8669 (tt0) cc_final: 0.8324 (tt0) REVERT: E 217 TYR cc_start: 0.8040 (m-80) cc_final: 0.7660 (m-10) REVERT: F 536 THR cc_start: 0.9331 (p) cc_final: 0.8783 (p) REVERT: F 540 GLN cc_start: 0.8878 (mp10) cc_final: 0.8514 (mp10) REVERT: F 625 ASN cc_start: 0.7996 (t0) cc_final: 0.7700 (t0) REVERT: I 6 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: I 36 TRP cc_start: 0.9468 (m100) cc_final: 0.8733 (m100) REVERT: L 35 TRP cc_start: 0.9196 (m100) cc_final: 0.8896 (m100) REVERT: M 49 TYR cc_start: 0.8611 (p90) cc_final: 0.7909 (p90) REVERT: N 49 TYR cc_start: 0.8418 (p90) cc_final: 0.8074 (p90) REVERT: N 81 GLU cc_start: 0.8332 (pm20) cc_final: 0.8129 (pm20) REVERT: N 103 THR cc_start: 0.9171 (p) cc_final: 0.8641 (p) outliers start: 52 outliers final: 48 residues processed: 403 average time/residue: 0.1146 time to fit residues: 76.9820 Evaluate side-chains 410 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 32 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN C 195 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067851 restraints weight = 56024.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070228 restraints weight = 25516.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071845 restraints weight = 15195.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072993 restraints weight = 10590.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073830 restraints weight = 8098.919| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20283 Z= 0.125 Angle : 0.651 11.360 27730 Z= 0.317 Chirality : 0.045 0.269 3293 Planarity : 0.003 0.039 3412 Dihedral : 5.577 57.273 4044 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.67 % Allowed : 20.12 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2358 helix: 1.32 (0.27), residues: 444 sheet: 0.47 (0.18), residues: 768 loop : -0.22 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 42 TYR 0.027 0.002 TYR L 49 PHE 0.011 0.001 PHE H 35D TRP 0.057 0.002 TRP M 35 HIS 0.016 0.001 HIS N 37 Details of bonding type rmsd covalent geometry : bond 0.00290 (20174) covalent geometry : angle 0.62524 (27442) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.45916 ( 78) hydrogen bonds : bond 0.03175 ( 744) hydrogen bonds : angle 4.69528 ( 2106) link_BETA1-4 : bond 0.00371 ( 22) link_BETA1-4 : angle 1.48707 ( 66) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.21705 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.25 seconds wall clock time: 47 minutes 7.99 seconds (2827.99 seconds total)