Starting phenix.real_space_refine on Tue Jun 17 12:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ult_42365/06_2025/8ult_42365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ult_42365/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ult_42365/06_2025/8ult_42365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ult_42365/06_2025/8ult_42365.map" model { file = "/net/cci-nas-00/data/ceres_data/8ult_42365/06_2025/8ult_42365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ult_42365/06_2025/8ult_42365.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 4, '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: {'GLN:plan1': 1, 'ARG:plan': 4, '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: {'GLN:plan1': 1, 'ARG:plan': 4, '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: 13.14, per 1000 atoms: 0.67 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: 5.66 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.92 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: 9.20 Time building geometry restraints manager: 6.53 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 504 or resid 601 through 609)) selection = (chain 'C' and (resid 33 through 504 or resid 601 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 49.580 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.390 ------------------------------------------------------------------------------- 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 : 10.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.020 0.002 TRP C 479 HIS 0.005 0.001 HIS A 374 PHE 0.009 0.001 PHE L 71 TYR 0.030 0.002 TYR L 49 ARG 0.017 0.001 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 48) link_NAG-ASN : angle 2.55393 ( 144) link_BETA1-4 : bond 0.01138 ( 22) link_BETA1-4 : angle 2.38900 ( 66) hydrogen bonds : bond 0.20201 ( 744) hydrogen bonds : angle 8.76275 ( 2106) SS BOND : bond 0.00538 ( 39) SS BOND : angle 1.57562 ( 78) covalent geometry : bond 0.00503 (20174) covalent geometry : angle 0.69980 (27442) *********************** 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 : 2.352 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: B 625 ASN cc_start: 0.8143 (t0) cc_final: 0.7901 (t0) REVERT: B 646 LEU cc_start: 0.9642 (mt) cc_final: 0.9435 (mt) REVERT: C 475 MET cc_start: 0.8919 (mmm) cc_final: 0.8506 (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: 0.8881 (t80) REVERT: D 625 ASN cc_start: 0.8145 (t0) cc_final: 0.7767 (t0) REVERT: E 475 MET cc_start: 0.8933 (mmm) cc_final: 0.8477 (mmt) REVERT: F 536 THR cc_start: 0.9258 (p) cc_final: 0.8807 (p) REVERT: F 540 GLN cc_start: 0.8999 (mp10) cc_final: 0.8699 (mp10) REVERT: F 591 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8839 (tt0) REVERT: F 625 ASN cc_start: 0.8210 (t0) cc_final: 0.7980 (t0) REVERT: H 72 ASP cc_start: 0.8548 (t0) cc_final: 0.8093 (t0) REVERT: I 59 TYR cc_start: 0.8181 (m-10) cc_final: 0.7904 (m-80) REVERT: I 72 ASP cc_start: 0.8475 (t0) cc_final: 0.8062 (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: 0.8432 (p) REVERT: J 91 TYR cc_start: 0.9095 (m-80) cc_final: 0.8756 (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: 0.8934 (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: 0.7731 (m-30) REVERT: M 103 THR cc_start: 0.9326 (p) cc_final: 0.9106 (p) REVERT: N 49 TYR cc_start: 0.8754 (p90) cc_final: 0.8327 (p90) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.2872 time to fit residues: 218.1715 Evaluate side-chains 372 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3209 r_free = 0.3209 target = 0.079344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.067092 restraints weight = 56160.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.069481 restraints weight = 26508.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071067 restraints weight = 16131.758| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20283 Z= 0.248 Angle : 0.701 11.102 27730 Z= 0.347 Chirality : 0.048 0.219 3293 Planarity : 0.004 0.042 3412 Dihedral : 9.013 67.792 4044 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.62 % Allowed : 11.42 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2358 helix: 1.17 (0.26), residues: 438 sheet: 0.13 (0.18), residues: 822 loop : -0.43 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.011 0.001 HIS L 37 PHE 0.021 0.002 PHE A 233 TYR 0.020 0.002 TYR B 586 ARG 0.006 0.001 ARG E 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 48) link_NAG-ASN : angle 2.77504 ( 144) link_BETA1-4 : bond 0.00381 ( 22) link_BETA1-4 : angle 2.12523 ( 66) hydrogen bonds : bond 0.04524 ( 744) hydrogen bonds : angle 6.04795 ( 2106) SS BOND : bond 0.00506 ( 39) SS BOND : angle 1.34590 ( 78) covalent geometry : bond 0.00558 (20174) covalent geometry : angle 0.66335 (27442) *********************** 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 446 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 392 time to evaluate : 2.079 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 475 MET cc_start: 0.9090 (mmm) cc_final: 0.8888 (mmm) REVERT: A 484 TYR cc_start: 0.9216 (p90) cc_final: 0.8775 (p90) REVERT: B 535 MET cc_start: 0.9283 (mmm) cc_final: 0.9020 (mmm) REVERT: B 571 TRP cc_start: 0.8885 (m100) cc_final: 0.8654 (m100) REVERT: B 591 GLN cc_start: 0.9076 (tp40) cc_final: 0.8709 (tp40) REVERT: B 625 ASN cc_start: 0.8271 (t0) cc_final: 0.7947 (t0) REVERT: C 180 ASP cc_start: 0.8729 (m-30) cc_final: 0.8496 (t0) REVERT: C 466 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7520 (mt-10) REVERT: D 621 GLU cc_start: 0.8884 (tp30) cc_final: 0.8618 (tp30) REVERT: E 271 MET cc_start: 0.7853 (mtp) cc_final: 0.7564 (mtp) REVERT: F 536 THR cc_start: 0.9272 (p) cc_final: 0.8822 (p) REVERT: F 540 GLN cc_start: 0.9049 (mp10) cc_final: 0.8707 (mp10) REVERT: F 621 GLU cc_start: 0.8873 (tp30) cc_final: 0.8580 (tp30) REVERT: F 625 ASN cc_start: 0.8061 (t0) cc_final: 0.7842 (t0) REVERT: F 658 GLN cc_start: 0.9280 (tt0) cc_final: 0.9034 (tt0) REVERT: H 79 TYR cc_start: 0.9369 (m-80) cc_final: 0.9148 (m-10) REVERT: J 79 TYR cc_start: 0.9284 (m-80) cc_final: 0.9079 (m-10) REVERT: J 89 THR cc_start: 0.8903 (p) cc_final: 0.8434 (t) REVERT: J 91 TYR cc_start: 0.9159 (m-80) cc_final: 0.8584 (m-80) REVERT: M 49 TYR cc_start: 0.8616 (p90) cc_final: 0.7690 (p90) REVERT: N 27 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7076 (tm-30) REVERT: N 36 TYR cc_start: 0.9078 (m-80) cc_final: 0.8693 (m-10) REVERT: N 49 TYR cc_start: 0.8626 (p90) cc_final: 0.8154 (p90) REVERT: N 79 LEU cc_start: 0.8104 (mp) cc_final: 0.7796 (mt) REVERT: N 81 GLU cc_start: 0.8366 (pm20) cc_final: 0.8081 (pm20) outliers start: 54 outliers final: 41 residues processed: 419 average time/residue: 0.2741 time to fit residues: 185.4832 Evaluate side-chains 389 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 434 MET 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 E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 201 ILE 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 I residue 51 VAL Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 51 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 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 65 SER 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 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 203 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 30 optimal weight: 0.0980 chunk 218 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.068796 restraints weight = 55612.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.071107 restraints weight = 25362.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072771 restraints weight = 15235.280| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20283 Z= 0.206 Angle : 0.659 11.077 27730 Z= 0.326 Chirality : 0.047 0.297 3293 Planarity : 0.004 0.041 3412 Dihedral : 7.686 59.912 4044 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.92 % Allowed : 13.65 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2358 helix: 1.22 (0.26), residues: 438 sheet: 0.29 (0.18), residues: 735 loop : -0.49 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 479 HIS 0.006 0.001 HIS N 37 PHE 0.015 0.001 PHE C 53 TYR 0.023 0.002 TYR I 59 ARG 0.006 0.000 ARG E 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 48) link_NAG-ASN : angle 2.65284 ( 144) link_BETA1-4 : bond 0.00359 ( 22) link_BETA1-4 : angle 1.99261 ( 66) hydrogen bonds : bond 0.04127 ( 744) hydrogen bonds : angle 5.54682 ( 2106) SS BOND : bond 0.00463 ( 39) SS BOND : angle 1.64466 ( 78) covalent geometry : bond 0.00469 (20174) covalent geometry : angle 0.61991 (27442) *********************** 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 442 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 382 time to evaluate : 2.321 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: 0.8919 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 484 TYR cc_start: 0.9275 (p90) cc_final: 0.8958 (p90) REVERT: B 571 TRP cc_start: 0.8896 (m100) cc_final: 0.8652 (m100) REVERT: B 591 GLN cc_start: 0.9084 (tp40) cc_final: 0.8667 (tp40) REVERT: B 625 ASN cc_start: 0.8230 (t0) cc_final: 0.7932 (t0) REVERT: C 475 MET cc_start: 0.9024 (mmm) cc_final: 0.8725 (mmt) REVERT: D 540 GLN cc_start: 0.8755 (mp10) cc_final: 0.8509 (mp10) REVERT: D 586 TYR cc_start: 0.9503 (t80) cc_final: 0.9006 (t80) REVERT: D 606 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9170 (p) REVERT: D 625 ASN cc_start: 0.8059 (t0) cc_final: 0.7835 (t0) REVERT: D 650 GLN cc_start: 0.9487 (tp40) cc_final: 0.8653 (tm-30) REVERT: D 654 GLU cc_start: 0.8688 (tt0) cc_final: 0.8447 (tt0) REVERT: E 217 TYR cc_start: 0.8012 (m-80) cc_final: 0.7677 (m-80) REVERT: E 323 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9092 (mp) REVERT: E 432 GLN cc_start: 0.8941 (mt0) cc_final: 0.8702 (mt0) REVERT: E 475 MET cc_start: 0.9203 (mmt) cc_final: 0.8970 (mmt) REVERT: F 536 THR cc_start: 0.9289 (p) cc_final: 0.8831 (p) REVERT: F 540 GLN cc_start: 0.9074 (mp10) cc_final: 0.8756 (mp10) REVERT: F 621 GLU cc_start: 0.8840 (tp30) cc_final: 0.8610 (tp30) REVERT: F 625 ASN cc_start: 0.8176 (t0) cc_final: 0.7825 (t0) REVERT: F 658 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8937 (tt0) REVERT: H 6 GLN cc_start: 0.8292 (mt0) cc_final: 0.7984 (tt0) REVERT: H 79 TYR cc_start: 0.9363 (m-80) cc_final: 0.9146 (m-10) REVERT: M 49 TYR cc_start: 0.8618 (p90) cc_final: 0.7827 (p90) REVERT: M 82 ASP cc_start: 0.8383 (m-30) cc_final: 0.8164 (m-30) REVERT: N 27 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7075 (tm-30) REVERT: N 49 TYR cc_start: 0.8606 (p90) cc_final: 0.8118 (p90) REVERT: N 79 LEU cc_start: 0.8180 (mp) cc_final: 0.7855 (mt) REVERT: N 81 GLU cc_start: 0.8389 (pm20) cc_final: 0.8185 (pm20) outliers start: 60 outliers final: 43 residues processed: 419 average time/residue: 0.2755 time to fit residues: 188.2456 Evaluate side-chains 388 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 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 296 CYS Chi-restraints excluded: chain C residue 373 THR 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 323 ILE 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 F residue 624 ASP Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain L residue 60 SER 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 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 132 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN J 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066180 restraints weight = 56563.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068555 restraints weight = 26421.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.070215 restraints weight = 15992.899| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20283 Z= 0.219 Angle : 0.667 11.079 27730 Z= 0.328 Chirality : 0.047 0.300 3293 Planarity : 0.004 0.040 3412 Dihedral : 7.047 59.775 4044 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.79 % Allowed : 15.31 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2358 helix: 1.28 (0.26), residues: 438 sheet: 0.33 (0.18), residues: 777 loop : -0.50 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 571 HIS 0.014 0.001 HIS N 37 PHE 0.017 0.001 PHE C 53 TYR 0.026 0.002 TYR J 59 ARG 0.004 0.000 ARG M 104 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 2.64694 ( 144) link_BETA1-4 : bond 0.00342 ( 22) link_BETA1-4 : angle 1.87417 ( 66) hydrogen bonds : bond 0.03905 ( 744) hydrogen bonds : angle 5.34325 ( 2106) SS BOND : bond 0.00481 ( 39) SS BOND : angle 1.69516 ( 78) covalent geometry : bond 0.00497 (20174) covalent geometry : angle 0.62996 (27442) *********************** 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 455 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 377 time to evaluate : 2.118 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: 0.8914 (OUTLIER) cc_final: 0.8546 (p) REVERT: A 484 TYR cc_start: 0.9282 (p90) cc_final: 0.9045 (p90) REVERT: B 571 TRP cc_start: 0.8939 (m100) cc_final: 0.8687 (m100) REVERT: B 591 GLN cc_start: 0.9074 (tp40) cc_final: 0.8687 (tp40) REVERT: B 625 ASN cc_start: 0.8210 (t0) cc_final: 0.7914 (t0) REVERT: D 540 GLN cc_start: 0.8733 (mp10) cc_final: 0.8463 (mp10) REVERT: D 586 TYR cc_start: 0.9534 (t80) cc_final: 0.9092 (t80) REVERT: D 650 GLN cc_start: 0.9481 (tp40) cc_final: 0.8666 (tm-30) REVERT: D 654 GLU cc_start: 0.8692 (tt0) cc_final: 0.8410 (tt0) REVERT: E 217 TYR cc_start: 0.8132 (m-80) cc_final: 0.7767 (m-10) REVERT: E 323 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9082 (mp) REVERT: E 432 GLN cc_start: 0.9031 (mt0) cc_final: 0.8669 (mt0) REVERT: F 536 THR cc_start: 0.9305 (p) cc_final: 0.8851 (p) REVERT: F 540 GLN cc_start: 0.9084 (mp10) cc_final: 0.8745 (mp10) REVERT: F 621 GLU cc_start: 0.8825 (tp30) cc_final: 0.8611 (tp30) REVERT: F 625 ASN cc_start: 0.8124 (t0) cc_final: 0.7712 (t0) REVERT: F 658 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.8977 (tt0) REVERT: F 659 ASP cc_start: 0.8843 (t0) cc_final: 0.8640 (t0) REVERT: H 6 GLN cc_start: 0.8266 (mt0) cc_final: 0.8042 (tt0) REVERT: J 59 TYR cc_start: 0.8489 (m-80) cc_final: 0.8259 (m-10) REVERT: M 49 TYR cc_start: 0.8660 (p90) cc_final: 0.7903 (p90) REVERT: M 61 ARG cc_start: 0.7081 (ptm-80) cc_final: 0.6836 (ptm-80) REVERT: N 27 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7097 (tm-30) REVERT: N 49 TYR cc_start: 0.8623 (p90) cc_final: 0.8074 (p90) REVERT: N 79 LEU cc_start: 0.8103 (mp) cc_final: 0.7813 (mt) REVERT: N 82 ASP cc_start: 0.8163 (m-30) cc_final: 0.7671 (m-30) REVERT: N 89 GLN cc_start: 0.9148 (tt0) cc_final: 0.8679 (tt0) outliers start: 78 outliers final: 56 residues processed: 426 average time/residue: 0.2687 time to fit residues: 186.4975 Evaluate side-chains 409 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 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 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 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 529 THR Chi-restraints excluded: chain F residue 544 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 F residue 658 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 89 THR 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 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 158 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 210 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.064977 restraints weight = 55584.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.067304 restraints weight = 25974.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068944 restraints weight = 15815.423| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20283 Z= 0.206 Angle : 0.661 11.065 27730 Z= 0.325 Chirality : 0.047 0.288 3293 Planarity : 0.004 0.041 3412 Dihedral : 6.778 59.658 4044 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.69 % Allowed : 16.76 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2358 helix: 1.45 (0.27), residues: 420 sheet: 0.22 (0.18), residues: 798 loop : -0.41 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 571 HIS 0.010 0.001 HIS N 37 PHE 0.016 0.001 PHE B 519 TYR 0.019 0.002 TYR F 586 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 48) link_NAG-ASN : angle 2.59249 ( 144) link_BETA1-4 : bond 0.00345 ( 22) link_BETA1-4 : angle 1.79314 ( 66) hydrogen bonds : bond 0.03799 ( 744) hydrogen bonds : angle 5.21550 ( 2106) SS BOND : bond 0.00470 ( 39) SS BOND : angle 1.60246 ( 78) covalent geometry : bond 0.00470 (20174) covalent geometry : angle 0.62557 (27442) *********************** 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 454 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 378 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8733 (m-30) cc_final: 0.8488 (m-30) REVERT: A 163 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 484 TYR cc_start: 0.9298 (p90) cc_final: 0.9029 (p90) REVERT: B 571 TRP cc_start: 0.8954 (m100) cc_final: 0.8714 (m100) REVERT: B 591 GLN cc_start: 0.9087 (tp40) cc_final: 0.8704 (tp40) REVERT: B 621 GLU cc_start: 0.8861 (tp30) cc_final: 0.8573 (tp30) REVERT: B 625 ASN cc_start: 0.8231 (t0) cc_final: 0.7837 (t0) REVERT: C 180 ASP cc_start: 0.8622 (m-30) cc_final: 0.8393 (t0) REVERT: C 475 MET cc_start: 0.9064 (mmm) cc_final: 0.8822 (mmt) REVERT: D 586 TYR cc_start: 0.9529 (t80) cc_final: 0.9062 (t80) REVERT: D 625 ASN cc_start: 0.8120 (t0) cc_final: 0.7764 (t0) REVERT: D 650 GLN cc_start: 0.9480 (tp40) cc_final: 0.8718 (tm-30) REVERT: D 654 GLU cc_start: 0.8714 (tt0) cc_final: 0.8419 (tt0) REVERT: E 217 TYR cc_start: 0.8187 (m-80) cc_final: 0.7758 (m-10) REVERT: E 323 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9064 (mp) REVERT: E 432 GLN cc_start: 0.9024 (mt0) cc_final: 0.8664 (mt0) REVERT: F 536 THR cc_start: 0.9302 (p) cc_final: 0.8860 (p) REVERT: F 540 GLN cc_start: 0.9084 (mp10) cc_final: 0.8738 (mp10) REVERT: F 625 ASN cc_start: 0.8138 (t0) cc_final: 0.7733 (t0) REVERT: F 659 ASP cc_start: 0.8841 (t0) cc_final: 0.8623 (t0) REVERT: M 49 TYR cc_start: 0.8691 (p90) cc_final: 0.7967 (p90) REVERT: M 82 ASP cc_start: 0.8173 (m-30) cc_final: 0.7964 (m-30) REVERT: N 27 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7188 (tm-30) REVERT: N 49 TYR cc_start: 0.8631 (p90) cc_final: 0.8157 (p90) outliers start: 76 outliers final: 63 residues processed: 426 average time/residue: 0.2812 time to fit residues: 196.7648 Evaluate side-chains 411 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 346 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU 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 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 54 CYS 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 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 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 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 544 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 H residue 67 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 105 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 4 VAL Chi-restraints excluded: chain L residue 12 SER 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 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 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 60 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067011 restraints weight = 56333.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.069391 restraints weight = 26356.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071058 restraints weight = 15948.932| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20283 Z= 0.167 Angle : 0.649 11.013 27730 Z= 0.319 Chirality : 0.046 0.282 3293 Planarity : 0.003 0.040 3412 Dihedral : 6.493 58.570 4044 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.50 % Allowed : 17.83 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2358 helix: 1.54 (0.27), residues: 420 sheet: 0.34 (0.18), residues: 780 loop : -0.39 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 571 HIS 0.024 0.001 HIS N 37 PHE 0.017 0.001 PHE F 519 TYR 0.028 0.002 TYR J 59 ARG 0.004 0.000 ARG E 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 48) link_NAG-ASN : angle 2.49914 ( 144) link_BETA1-4 : bond 0.00352 ( 22) link_BETA1-4 : angle 1.69482 ( 66) hydrogen bonds : bond 0.03607 ( 744) hydrogen bonds : angle 5.09619 ( 2106) SS BOND : bond 0.00468 ( 39) SS BOND : angle 1.56984 ( 78) covalent geometry : bond 0.00382 (20174) covalent geometry : angle 0.61583 (27442) *********************** 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 449 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 377 time to evaluate : 2.564 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 104 MET cc_start: 0.9257 (ttm) cc_final: 0.8817 (tpp) REVERT: A 163 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 479 TRP cc_start: 0.8627 (m-10) cc_final: 0.8293 (m-90) REVERT: B 571 TRP cc_start: 0.8919 (m100) cc_final: 0.8716 (m100) REVERT: B 591 GLN cc_start: 0.9046 (tp40) cc_final: 0.8660 (tp40) REVERT: B 621 GLU cc_start: 0.8818 (tp30) cc_final: 0.8545 (tp30) REVERT: B 625 ASN cc_start: 0.8201 (t0) cc_final: 0.7833 (t0) REVERT: C 180 ASP cc_start: 0.8578 (m-30) cc_final: 0.8344 (t0) REVERT: D 586 TYR cc_start: 0.9519 (t80) cc_final: 0.9063 (t80) REVERT: D 650 GLN cc_start: 0.9460 (tp40) cc_final: 0.8736 (tm-30) REVERT: D 654 GLU cc_start: 0.8657 (tt0) cc_final: 0.8344 (tt0) REVERT: E 217 TYR cc_start: 0.8119 (m-80) cc_final: 0.7789 (m-10) REVERT: E 323 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9052 (mp) REVERT: E 432 GLN cc_start: 0.9012 (mt0) cc_final: 0.8616 (mt0) REVERT: F 536 THR cc_start: 0.9284 (p) cc_final: 0.8833 (p) REVERT: F 540 GLN cc_start: 0.9055 (mp10) cc_final: 0.8706 (mp10) REVERT: F 621 GLU cc_start: 0.8859 (tp30) cc_final: 0.8597 (tp30) REVERT: F 625 ASN cc_start: 0.8120 (t0) cc_final: 0.7794 (t0) REVERT: F 659 ASP cc_start: 0.8823 (t0) cc_final: 0.8600 (t0) REVERT: M 49 TYR cc_start: 0.8676 (p90) cc_final: 0.7907 (p90) REVERT: N 27 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7258 (tm-30) REVERT: N 49 TYR cc_start: 0.8597 (p90) cc_final: 0.8146 (p90) outliers start: 72 outliers final: 62 residues processed: 419 average time/residue: 0.3820 time to fit residues: 260.8261 Evaluate side-chains 417 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE 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 595 ILE Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 54 CYS 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 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 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 323 ILE 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 67 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 89 THR 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 90 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 54 LEU 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 119 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 233 optimal weight: 0.9990 chunk 195 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068920 restraints weight = 55268.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.071364 restraints weight = 25480.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073041 restraints weight = 15222.644| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2657 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= 0.120 Angle : 0.634 11.733 27730 Z= 0.310 Chirality : 0.046 0.269 3293 Planarity : 0.003 0.040 3412 Dihedral : 6.075 58.269 4044 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.62 % Allowed : 19.53 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2358 helix: 1.33 (0.27), residues: 447 sheet: 0.42 (0.18), residues: 768 loop : -0.35 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP M 35 HIS 0.015 0.001 HIS N 37 PHE 0.014 0.001 PHE B 519 TYR 0.024 0.002 TYR F 586 ARG 0.007 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.33665 ( 144) link_BETA1-4 : bond 0.00389 ( 22) link_BETA1-4 : angle 1.57463 ( 66) hydrogen bonds : bond 0.03311 ( 744) hydrogen bonds : angle 4.93303 ( 2106) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.49053 ( 78) covalent geometry : bond 0.00274 (20174) covalent geometry : angle 0.60402 (27442) *********************** 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 457 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 403 time to evaluate : 2.142 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: 0.8771 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 479 TRP cc_start: 0.8553 (m-10) cc_final: 0.8303 (m-90) REVERT: B 591 GLN cc_start: 0.8992 (tp40) cc_final: 0.8626 (tp40) REVERT: B 621 GLU cc_start: 0.8845 (tp30) cc_final: 0.8620 (tp30) REVERT: B 625 ASN cc_start: 0.8165 (t0) cc_final: 0.7828 (t0) REVERT: D 530 MET cc_start: 0.8632 (tpp) cc_final: 0.8400 (tpp) REVERT: D 537 LEU cc_start: 0.9460 (mt) cc_final: 0.9116 (mt) REVERT: D 586 TYR cc_start: 0.9488 (t80) cc_final: 0.9074 (t80) REVERT: D 625 ASN cc_start: 0.8049 (t0) cc_final: 0.7777 (t0) REVERT: D 650 GLN cc_start: 0.9439 (tp40) cc_final: 0.8782 (tm-30) REVERT: D 654 GLU cc_start: 0.8664 (tt0) cc_final: 0.8346 (tt0) REVERT: E 217 TYR cc_start: 0.7952 (m-80) cc_final: 0.7672 (m-10) REVERT: E 432 GLN cc_start: 0.9017 (mt0) cc_final: 0.8467 (mt0) REVERT: F 536 THR cc_start: 0.9260 (p) cc_final: 0.8811 (p) REVERT: F 540 GLN cc_start: 0.9030 (mp10) cc_final: 0.8686 (mp10) REVERT: F 621 GLU cc_start: 0.8819 (tp30) cc_final: 0.8593 (tp30) REVERT: F 625 ASN cc_start: 0.8122 (t0) cc_final: 0.7779 (t0) REVERT: F 659 ASP cc_start: 0.8837 (t0) cc_final: 0.8602 (t0) REVERT: H 36 TRP cc_start: 0.9382 (m100) cc_final: 0.8967 (m100) REVERT: L 35 TRP cc_start: 0.9322 (m100) cc_final: 0.9013 (m100) REVERT: M 49 TYR cc_start: 0.8611 (p90) cc_final: 0.7907 (p90) REVERT: N 27 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7327 (tm-30) REVERT: N 49 TYR cc_start: 0.8551 (p90) cc_final: 0.8043 (p90) REVERT: N 70 TYR cc_start: 0.8364 (t80) cc_final: 0.8162 (t80) outliers start: 54 outliers final: 47 residues processed: 435 average time/residue: 0.2915 time to fit residues: 204.7629 Evaluate side-chains 417 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 369 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 LEU 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 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 247 CYS 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 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 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 H residue 67 ILE Chi-restraints excluded: chain I 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 67 VAL Chi-restraints excluded: chain L residue 74 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 136 ASN C 195 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 6 GLN ** M 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 = 0.3157 r_free = 0.3157 target = 0.076105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.064451 restraints weight = 55951.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.066770 restraints weight = 26500.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.068395 restraints weight = 16139.578| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20283 Z= 0.255 Angle : 0.714 11.134 27730 Z= 0.348 Chirality : 0.047 0.290 3293 Planarity : 0.004 0.042 3412 Dihedral : 6.443 57.375 4044 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.69 % Allowed : 19.53 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2358 helix: 1.52 (0.27), residues: 417 sheet: 0.17 (0.18), residues: 813 loop : -0.21 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP M 35 HIS 0.015 0.002 HIS N 37 PHE 0.016 0.002 PHE M 62 TYR 0.021 0.002 TYR I 59 ARG 0.004 0.000 ARG E 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 48) link_NAG-ASN : angle 2.61058 ( 144) link_BETA1-4 : bond 0.00325 ( 22) link_BETA1-4 : angle 1.82915 ( 66) hydrogen bonds : bond 0.03722 ( 744) hydrogen bonds : angle 5.07828 ( 2106) SS BOND : bond 0.00491 ( 39) SS BOND : angle 1.60089 ( 78) covalent geometry : bond 0.00582 (20174) covalent geometry : angle 0.68087 (27442) *********************** 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 422 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 2.277 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: 0.8810 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 479 TRP cc_start: 0.8659 (m-10) cc_final: 0.8340 (m-90) REVERT: B 591 GLN cc_start: 0.9096 (tp40) cc_final: 0.8707 (tp40) REVERT: B 621 GLU cc_start: 0.8847 (tp30) cc_final: 0.8632 (tp30) REVERT: B 625 ASN cc_start: 0.8247 (t0) cc_final: 0.7830 (t0) REVERT: C 180 ASP cc_start: 0.8570 (m-30) cc_final: 0.8331 (t0) REVERT: D 586 TYR cc_start: 0.9561 (t80) cc_final: 0.9104 (t80) REVERT: D 625 ASN cc_start: 0.8053 (t0) cc_final: 0.7732 (t0) REVERT: D 650 GLN cc_start: 0.9496 (tp40) cc_final: 0.8807 (tm-30) REVERT: D 654 GLU cc_start: 0.8652 (tt0) cc_final: 0.8359 (tt0) REVERT: E 217 TYR cc_start: 0.8365 (m-80) cc_final: 0.7822 (m-10) REVERT: E 323 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9044 (mp) REVERT: E 432 GLN cc_start: 0.9052 (mt0) cc_final: 0.8599 (mt0) REVERT: F 621 GLU cc_start: 0.8855 (tp30) cc_final: 0.8545 (tp30) REVERT: F 625 ASN cc_start: 0.8175 (t0) cc_final: 0.7741 (t0) REVERT: F 659 ASP cc_start: 0.8840 (t0) cc_final: 0.8612 (t0) REVERT: M 49 TYR cc_start: 0.8758 (p90) cc_final: 0.7946 (p90) REVERT: N 27 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7534 (tm-30) REVERT: N 49 TYR cc_start: 0.8666 (p90) cc_final: 0.8309 (p90) outliers start: 76 outliers final: 63 residues processed: 393 average time/residue: 0.2959 time to fit residues: 192.0120 Evaluate side-chains 406 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 341 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE 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 544 LEU 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 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 323 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 544 LEU 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 67 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 6 GLN 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 65 SER Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR 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 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 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 89 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 135 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 226 optimal weight: 0.1980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 136 ASN C 195 ASN D 543 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** 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 = 0.3189 r_free = 0.3189 target = 0.078290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.066480 restraints weight = 56293.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068865 restraints weight = 25883.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.070498 restraints weight = 15404.386| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2872 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= 0.124 Angle : 0.662 13.386 27730 Z= 0.322 Chirality : 0.046 0.269 3293 Planarity : 0.003 0.039 3412 Dihedral : 6.051 58.771 4044 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.92 % Allowed : 20.55 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2358 helix: 1.47 (0.27), residues: 429 sheet: 0.37 (0.18), residues: 780 loop : -0.29 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 35 HIS 0.023 0.001 HIS N 37 PHE 0.015 0.001 PHE B 519 TYR 0.015 0.002 TYR L 70 ARG 0.003 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 48) link_NAG-ASN : angle 2.34856 ( 144) link_BETA1-4 : bond 0.00405 ( 22) link_BETA1-4 : angle 1.56862 ( 66) hydrogen bonds : bond 0.03366 ( 744) hydrogen bonds : angle 4.88798 ( 2106) SS BOND : bond 0.00451 ( 39) SS BOND : angle 1.52025 ( 78) covalent geometry : bond 0.00284 (20174) covalent geometry : angle 0.63327 (27442) *********************** 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: 60 poor density : 391 time to evaluate : 2.560 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: 0.8700 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 479 TRP cc_start: 0.8534 (m-10) cc_final: 0.8292 (m-90) REVERT: B 591 GLN cc_start: 0.9015 (tp40) cc_final: 0.8730 (tp40) REVERT: B 621 GLU cc_start: 0.8869 (tp30) cc_final: 0.8629 (tp30) REVERT: B 625 ASN cc_start: 0.8212 (t0) cc_final: 0.7865 (t0) REVERT: C 180 ASP cc_start: 0.8585 (m-30) cc_final: 0.8286 (t0) REVERT: D 586 TYR cc_start: 0.9487 (t80) cc_final: 0.9188 (t80) REVERT: D 625 ASN cc_start: 0.8002 (t0) cc_final: 0.7728 (t0) REVERT: D 650 GLN cc_start: 0.9458 (tp40) cc_final: 0.8834 (tm-30) REVERT: D 654 GLU cc_start: 0.8695 (tt0) cc_final: 0.8351 (tt0) REVERT: E 217 TYR cc_start: 0.8104 (m-80) cc_final: 0.7751 (m-10) REVERT: E 323 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9070 (mp) REVERT: E 432 GLN cc_start: 0.9026 (mt0) cc_final: 0.8432 (mt0) REVERT: F 540 GLN cc_start: 0.9010 (mp10) cc_final: 0.8618 (mp10) REVERT: F 621 GLU cc_start: 0.8824 (tp30) cc_final: 0.8610 (tp30) REVERT: F 625 ASN cc_start: 0.8142 (t0) cc_final: 0.7724 (t0) REVERT: F 650 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8338 (tm-30) REVERT: F 659 ASP cc_start: 0.8852 (t0) cc_final: 0.8623 (t0) REVERT: I 100 ARG cc_start: 0.8723 (ttt180) cc_final: 0.8409 (ttt-90) REVERT: L 35 TRP cc_start: 0.9324 (m100) cc_final: 0.9043 (m100) REVERT: M 49 TYR cc_start: 0.8648 (p90) cc_final: 0.7826 (p90) REVERT: N 27 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7208 (tm-30) REVERT: N 49 TYR cc_start: 0.8547 (p90) cc_final: 0.8276 (p90) REVERT: N 103 THR cc_start: 0.9228 (p) cc_final: 0.8443 (p) outliers start: 60 outliers final: 52 residues processed: 428 average time/residue: 0.3866 time to fit residues: 267.2505 Evaluate side-chains 422 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 368 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE 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 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 323 ILE 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 51 VAL Chi-restraints excluded: chain H residue 67 ILE 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 I residue 67 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR 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 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 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 84 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** 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 = 0.3192 r_free = 0.3192 target = 0.078129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.066576 restraints weight = 56215.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068945 restraints weight = 26109.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.070601 restraints weight = 15598.041| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2946 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= 0.138 Angle : 0.665 12.117 27730 Z= 0.324 Chirality : 0.046 0.271 3293 Planarity : 0.003 0.039 3412 Dihedral : 5.923 57.327 4044 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.72 % Allowed : 21.04 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2358 helix: 1.47 (0.27), residues: 429 sheet: 0.31 (0.18), residues: 795 loop : -0.20 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 571 HIS 0.020 0.001 HIS N 37 PHE 0.016 0.001 PHE M 62 TYR 0.023 0.002 TYR N 70 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 48) link_NAG-ASN : angle 2.33714 ( 144) link_BETA1-4 : bond 0.00367 ( 22) link_BETA1-4 : angle 1.57840 ( 66) hydrogen bonds : bond 0.03340 ( 744) hydrogen bonds : angle 4.84435 ( 2106) SS BOND : bond 0.00428 ( 39) SS BOND : angle 1.53082 ( 78) covalent geometry : bond 0.00320 (20174) covalent geometry : angle 0.63702 (27442) ********************** 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 420 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (p) REVERT: A 479 TRP cc_start: 0.8582 (m-10) cc_final: 0.8278 (m-90) REVERT: B 591 GLN cc_start: 0.9013 (tp40) cc_final: 0.8720 (tp40) REVERT: B 621 GLU cc_start: 0.8844 (tp30) cc_final: 0.8602 (tp30) REVERT: B 625 ASN cc_start: 0.8175 (t0) cc_final: 0.7790 (t0) REVERT: C 180 ASP cc_start: 0.8544 (m-30) cc_final: 0.8219 (t0) REVERT: D 586 TYR cc_start: 0.9482 (t80) cc_final: 0.9182 (t80) REVERT: D 654 GLU cc_start: 0.8669 (tt0) cc_final: 0.8405 (tt0) REVERT: E 217 TYR cc_start: 0.8094 (m-80) cc_final: 0.7725 (m-10) REVERT: E 432 GLN cc_start: 0.9049 (mt0) cc_final: 0.8473 (mt0) REVERT: F 625 ASN cc_start: 0.8134 (t0) cc_final: 0.7753 (t0) REVERT: F 659 ASP cc_start: 0.8790 (t0) cc_final: 0.8550 (t0) REVERT: H 36 TRP cc_start: 0.9387 (m100) cc_final: 0.8998 (m100) REVERT: I 100 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8290 (ttt180) REVERT: L 35 TRP cc_start: 0.9261 (m100) cc_final: 0.9028 (m100) REVERT: L 103 THR cc_start: 0.9260 (p) cc_final: 0.8777 (p) REVERT: N 27 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7204 (tm-30) REVERT: N 49 TYR cc_start: 0.8552 (p90) cc_final: 0.8325 (p90) REVERT: N 103 THR cc_start: 0.9253 (p) cc_final: 0.8918 (p) outliers start: 56 outliers final: 52 residues processed: 401 average time/residue: 0.2722 time to fit residues: 178.2439 Evaluate side-chains 411 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 358 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 213 ILE 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 C residue 494 LEU 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 H residue 51 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 74 THR 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 27 GLN 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 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 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 59 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** 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 = 0.3187 r_free = 0.3187 target = 0.078251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.066494 restraints weight = 57163.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.068874 restraints weight = 26225.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070528 restraints weight = 15637.906| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 20283 Z= 0.215 Angle : 0.828 59.200 27730 Z= 0.444 Chirality : 0.046 0.272 3293 Planarity : 0.003 0.039 3412 Dihedral : 5.932 57.333 4044 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.82 % Allowed : 20.75 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2358 helix: 1.46 (0.27), residues: 429 sheet: 0.31 (0.18), residues: 795 loop : -0.20 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 571 HIS 0.017 0.001 HIS N 37 PHE 0.020 0.001 PHE H 63 TYR 0.022 0.002 TYR N 70 ARG 0.010 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 48) link_NAG-ASN : angle 2.33938 ( 144) link_BETA1-4 : bond 0.00363 ( 22) link_BETA1-4 : angle 1.58474 ( 66) hydrogen bonds : bond 0.03346 ( 744) hydrogen bonds : angle 4.84166 ( 2106) SS BOND : bond 0.00688 ( 39) SS BOND : angle 2.84230 ( 78) covalent geometry : bond 0.00506 (20174) covalent geometry : angle 0.79644 (27442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6535.65 seconds wall clock time: 119 minutes 39.88 seconds (7179.88 seconds total)