Starting phenix.real_space_refine on Fri Mar 6 06:52:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pz8_20527/03_2026/6pz8_20527.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 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 144 5.16 5 C 18096 2.51 5 N 4677 2.21 5 O 5766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28683 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "J" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: "f" 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: "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: "h" 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.85, per 1000 atoms: 0.24 Number of scatterers: 28683 At special positions: 0 Unit cell: (173.4, 186.66, 185.64, 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 144 16.00 O 5766 8.00 N 4677 7.00 C 18096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=1.76 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.08 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.02 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=1.76 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.04 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.08 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.04 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.02 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=1.76 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.04 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.08 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.03 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.04 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA a 3 " - " MAN a 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG B 801 " - " ASN B 719 " " NAG B 802 " - " ASN B 619 " " NAG B 803 " - " ASN B 66 " " NAG B 807 " - " ASN B 155 " " NAG B 817 " - " ASN B 244 " " NAG E1401 " - " ASN E 774 " " NAG F 801 " - " ASN F 719 " " NAG F 802 " - " ASN F 619 " " NAG F 803 " - " ASN F 66 " " NAG F 807 " - " ASN F 155 " " NAG F 817 " - " ASN F 244 " " NAG I1401 " - " ASN I 774 " " NAG J 801 " - " ASN J 719 " " NAG J 802 " - " ASN J 619 " " NAG J 803 " - " ASN J 66 " " NAG J 807 " - " ASN J 155 " " NAG J 817 " - " ASN J 244 " " NAG M 1 " - " ASN A 785 " " NAG N 1 " - " ASN A1176 " " NAG O 1 " - " ASN A 870 " " NAG P 1 " - " ASN A1213 " " NAG Q 1 " - " ASN B 125 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 222 " " NAG T 1 " - " ASN B 236 " " NAG U 1 " - " ASN E 785 " " NAG V 1 " - " ASN E1176 " " NAG W 1 " - " ASN E 870 " " NAG X 1 " - " ASN E1213 " " NAG Y 1 " - " ASN J 125 " " NAG Z 1 " - " ASN J 166 " " NAG a 1 " - " ASN J 222 " " NAG b 1 " - " ASN J 236 " " NAG c 1 " - " ASN I 785 " " NAG d 1 " - " ASN I1176 " " NAG e 1 " - " ASN I 870 " " NAG f 1 " - " ASN I1213 " " NAG g 1 " - " ASN F 125 " " NAG h 1 " - " ASN F 166 " " NAG i 1 " - " ASN F 222 " " NAG j 1 " - " ASN F 236 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 69 sheets defined 24.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET A 913 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 939 through 953 removed outlier: 4.040A pdb=" N MET A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS B 679 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 680 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS E 811 " --> pdb=" O LYS E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 852 " --> pdb=" O ASN E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 Processing helix chain 'E' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET E 913 " --> pdb=" O ASP E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 931 Processing helix chain 'E' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET E 943 " --> pdb=" O MET E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS E 995 " --> pdb=" O SER E 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU E 996 " --> pdb=" O GLU E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1007 through 1012 removed outlier: 3.990A pdb=" N PHE E1012 " --> pdb=" O MET E1008 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1039 Processing helix chain 'E' and resid 1040 through 1042 No H-bonds generated for 'chain 'E' and resid 1040 through 1042' Processing helix chain 'E' and resid 1050 through 1058 Processing helix chain 'E' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA E1065 " --> pdb=" O LEU E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1200 No H-bonds generated for 'chain 'E' and resid 1198 through 1200' Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 209 through 213 Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS J 679 " --> pdb=" O SER J 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU J 680 " --> pdb=" O VAL J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'I' and resid 805 through 811 removed outlier: 3.848A pdb=" N CYS I 811 " --> pdb=" O LYS I 807 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 822 Processing helix chain 'I' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS I 828 " --> pdb=" O TYR I 824 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 852 " --> pdb=" O ASN I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET I 913 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET I 943 " --> pdb=" O MET I 939 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS I 995 " --> pdb=" O SER I 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU I 996 " --> pdb=" O GLU I 992 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE I1012 " --> pdb=" O MET I1008 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 Processing helix chain 'I' and resid 1040 through 1042 No H-bonds generated for 'chain 'I' and resid 1040 through 1042' Processing helix chain 'I' and resid 1050 through 1058 Processing helix chain 'I' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA I1065 " --> pdb=" O LEU I1061 " (cutoff:3.500A) Processing helix chain 'I' and resid 1198 through 1200 No H-bonds generated for 'chain 'I' and resid 1198 through 1200' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 209 through 213 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS F 679 " --> pdb=" O SER F 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU F 680 " --> pdb=" O VAL F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE A 768 " --> pdb=" O SER E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.735A pdb=" N THR B 63 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU B 605 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY H 96 " --> pdb=" O MET H 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET H 100A" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU E 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 722 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE E 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL E1124 " --> pdb=" O VAL E1139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AD4, first strand: chain 'E' and resid 1202 through 1204 removed outlier: 5.508A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP J 34 " --> pdb=" O VAL J 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU J 180 " --> pdb=" O TYR J 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR J 241 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA J 182 " --> pdb=" O PHE J 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE J 239 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR J 184 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS J 237 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'J' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER J 215 " --> pdb=" O ASN J 218 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER J 362 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL J 661 " --> pdb=" O SER J 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER J 364 " --> pdb=" O VAL J 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 659 " --> pdb=" O SER J 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR C 33 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY C 96 " --> pdb=" O MET C 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET C 100A" --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET G 33 " --> pdb=" O HIS G 49 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU I 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 722 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU F 735 " --> pdb=" O LEU F 731 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'I' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN I1163 " --> pdb=" O ASP I1157 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP F 34 " --> pdb=" O VAL F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 83 through 85 removed outlier: 5.885A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR F 206 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU F 180 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR F 241 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA F 182 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 239 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR F 184 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS F 237 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'F' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER F 215 " --> pdb=" O ASN F 218 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER F 362 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL F 661 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER F 364 " --> pdb=" O VAL F 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 659 " --> pdb=" O SER F 364 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU F 605 " --> pdb=" O GLY F 372 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR D 33 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY D 96 " --> pdb=" O MET D 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET D 100A" --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS K 49 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5741 1.32 - 1.46: 9910 1.46 - 1.59: 13437 1.59 - 1.73: 33 1.73 - 1.87: 192 Bond restraints: 29313 Sorted by residual: bond pdb=" CG GLN F 280 " pdb=" CD GLN F 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" CG GLN J 280 " pdb=" CD GLN J 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CG GLN B 280 " pdb=" CD GLN B 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CB TYR J 58 " pdb=" CG TYR J 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 bond pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 ... (remaining 29308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 34247 2.51 - 5.01: 4779 5.01 - 7.52: 697 7.52 - 10.02: 83 10.02 - 12.53: 19 Bond angle restraints: 39825 Sorted by residual: angle pdb=" N GLU F 367 " pdb=" CA GLU F 367 " pdb=" C GLU F 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU J 367 " pdb=" CA GLU J 367 " pdb=" C GLU J 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU B 367 " pdb=" CA GLU B 367 " pdb=" C GLU B 367 " ideal model delta sigma weight residual 111.07 121.17 -10.10 1.07e+00 8.73e-01 8.91e+01 angle pdb=" N VAL E 802 " pdb=" CA VAL E 802 " pdb=" C VAL E 802 " ideal model delta sigma weight residual 108.45 120.98 -12.53 1.48e+00 4.57e-01 7.17e+01 angle pdb=" N VAL A 802 " pdb=" CA VAL A 802 " pdb=" C VAL A 802 " ideal model delta sigma weight residual 108.45 120.97 -12.52 1.48e+00 4.57e-01 7.15e+01 ... (remaining 39820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 17742 21.91 - 43.82: 396 43.82 - 65.72: 153 65.72 - 87.63: 81 87.63 - 109.54: 24 Dihedral angle restraints: 18396 sinusoidal: 8028 harmonic: 10368 Sorted by residual: dihedral pdb=" CB CYS B 727 " pdb=" SG CYS B 727 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.68 -46.68 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS F 727 " pdb=" SG CYS F 727 " pdb=" SG CYS F 736 " pdb=" CB CYS F 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS J 727 " pdb=" SG CYS J 727 " pdb=" SG CYS J 736 " pdb=" CB CYS J 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 18393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3078 0.093 - 0.185: 1200 0.185 - 0.278: 303 0.278 - 0.370: 56 0.370 - 0.463: 10 Chirality restraints: 4647 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4644 not shown) Planarity restraints: 5103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 66 " -0.061 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN F 66 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN F 66 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN F 66 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG F 803 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 66 " 0.061 2.00e-02 2.50e+03 6.35e-02 5.03e+01 pdb=" CG ASN J 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN J 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN J 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG J 803 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 66 " 0.061 2.00e-02 2.50e+03 6.34e-02 5.03e+01 pdb=" CG ASN B 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " 0.075 2.00e-02 2.50e+03 ... (remaining 5100 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6388 2.78 - 3.31: 26777 3.31 - 3.84: 50574 3.84 - 4.37: 61300 4.37 - 4.90: 97567 Nonbonded interactions: 242606 Sorted by model distance: nonbonded pdb=" OG SER J 328 " pdb=" OD1 ASP J 330 " model vdw 2.247 3.040 nonbonded pdb=" OG SER F 328 " pdb=" OD1 ASP F 330 " model vdw 2.247 3.040 nonbonded pdb=" OG SER B 328 " pdb=" OD1 ASP B 330 " model vdw 2.247 3.040 nonbonded pdb=" O4 NAG e 2 " pdb=" O6 NAG e 2 " model vdw 2.267 3.040 nonbonded pdb=" O4 NAG O 2 " pdb=" O6 NAG O 2 " model vdw 2.268 3.040 ... (remaining 242601 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } 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: 3.280 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.580 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 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 : 0.018 0.273 29433 Z= 0.955 Angle : 1.830 12.531 40143 Z= 1.200 Chirality : 0.103 0.463 4647 Planarity : 0.010 0.056 5061 Dihedral : 12.908 109.541 11658 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.22 % Favored : 96.19 % Rotamer: Outliers : 0.30 % Allowed : 1.02 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3543 helix: -0.19 (0.17), residues: 666 sheet: 0.21 (0.17), residues: 867 loop : 0.55 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I1088 TYR 0.074 0.010 TYR E 909 PHE 0.044 0.007 PHE I1012 TRP 0.031 0.008 TRP F 44 HIS 0.010 0.002 HIS A1146 Details of bonding type rmsd covalent geometry : bond 0.01759 (29313) covalent geometry : angle 1.81954 (39825) SS BOND : bond 0.07411 ( 42) SS BOND : angle 2.98151 ( 84) hydrogen bonds : bond 0.17085 ( 1154) hydrogen bonds : angle 7.41161 ( 3024) link_ALPHA1-3 : bond 0.07135 ( 3) link_ALPHA1-3 : angle 2.89356 ( 9) link_ALPHA1-6 : bond 0.05930 ( 3) link_ALPHA1-6 : angle 2.86095 ( 9) link_BETA1-4 : bond 0.05881 ( 30) link_BETA1-4 : angle 3.13746 ( 90) link_NAG-ASN : bond 0.04877 ( 42) link_NAG-ASN : angle 2.62562 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 627 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 808 GLN cc_start: 0.9180 (tp40) cc_final: 0.8764 (tp-100) REVERT: A 906 MET cc_start: 0.1475 (ttm) cc_final: 0.0215 (tmm) REVERT: A 1027 ASN cc_start: 0.8147 (m-40) cc_final: 0.7866 (m-40) REVERT: A 1074 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6648 (tpm170) REVERT: A 1126 PHE cc_start: 0.7280 (m-80) cc_final: 0.6766 (m-80) REVERT: B 18 TYR cc_start: 0.7902 (m-80) cc_final: 0.6361 (p90) REVERT: B 156 PHE cc_start: 0.7915 (m-80) cc_final: 0.7487 (m-80) REVERT: B 183 PHE cc_start: 0.9077 (p90) cc_final: 0.8776 (p90) REVERT: B 243 TYR cc_start: 0.8504 (m-80) cc_final: 0.7869 (m-80) REVERT: B 293 TYR cc_start: 0.6939 (p90) cc_final: 0.6548 (p90) REVERT: B 354 PHE cc_start: 0.5861 (p90) cc_final: 0.5636 (p90) REVERT: B 674 PHE cc_start: 0.8651 (m-80) cc_final: 0.8334 (m-80) REVERT: H 63 PHE cc_start: 0.4976 (m-80) cc_final: 0.4771 (m-80) REVERT: L 103 LYS cc_start: 0.6745 (tttt) cc_final: 0.6453 (mmtm) REVERT: E 808 GLN cc_start: 0.9218 (tp40) cc_final: 0.8828 (tp-100) REVERT: E 906 MET cc_start: 0.1885 (ttm) cc_final: 0.0994 (tmm) REVERT: E 1027 ASN cc_start: 0.8006 (m-40) cc_final: 0.7640 (m-40) REVERT: E 1074 ARG cc_start: 0.7523 (mmt90) cc_final: 0.6927 (tpp-160) REVERT: E 1126 PHE cc_start: 0.7307 (m-80) cc_final: 0.6879 (m-80) REVERT: J 18 TYR cc_start: 0.7989 (m-80) cc_final: 0.6205 (p90) REVERT: J 116 PHE cc_start: 0.7338 (p90) cc_final: 0.7131 (p90) REVERT: J 156 PHE cc_start: 0.7890 (m-80) cc_final: 0.7472 (m-80) REVERT: J 183 PHE cc_start: 0.9001 (p90) cc_final: 0.8706 (p90) REVERT: J 228 PHE cc_start: 0.9497 (t80) cc_final: 0.9212 (t80) REVERT: J 243 TYR cc_start: 0.8518 (m-80) cc_final: 0.7692 (m-80) REVERT: J 278 MET cc_start: 0.4808 (ttm) cc_final: 0.4542 (mtp) REVERT: J 293 TYR cc_start: 0.6695 (p90) cc_final: 0.6386 (p90) REVERT: J 632 TYR cc_start: 0.8285 (m-80) cc_final: 0.8082 (m-80) REVERT: J 674 PHE cc_start: 0.8579 (m-80) cc_final: 0.8284 (m-80) REVERT: C 82 PHE cc_start: 0.7965 (m-80) cc_final: 0.7628 (m-10) REVERT: G 103 LYS cc_start: 0.6567 (tttt) cc_final: 0.6342 (mmtm) REVERT: I 757 MET cc_start: 0.5570 (mtt) cc_final: 0.5260 (mmt) REVERT: I 808 GLN cc_start: 0.9171 (tp40) cc_final: 0.8752 (tp-100) REVERT: I 893 LEU cc_start: 0.8692 (mt) cc_final: 0.8283 (mt) REVERT: I 906 MET cc_start: 0.2209 (ttm) cc_final: 0.1152 (tmm) REVERT: I 1027 ASN cc_start: 0.8016 (m-40) cc_final: 0.7648 (m-40) REVERT: I 1123 ILE cc_start: 0.8830 (tp) cc_final: 0.8523 (tp) REVERT: I 1126 PHE cc_start: 0.7282 (m-80) cc_final: 0.6884 (m-80) REVERT: F 183 PHE cc_start: 0.9037 (p90) cc_final: 0.8700 (p90) REVERT: F 228 PHE cc_start: 0.9538 (t80) cc_final: 0.9300 (t80) REVERT: F 243 TYR cc_start: 0.8243 (m-80) cc_final: 0.7625 (m-80) REVERT: F 293 TYR cc_start: 0.6695 (p90) cc_final: 0.6345 (p90) REVERT: F 354 PHE cc_start: 0.5817 (p90) cc_final: 0.5565 (p90) REVERT: F 674 PHE cc_start: 0.8599 (m-80) cc_final: 0.8278 (m-80) REVERT: D 37 LEU cc_start: 0.6386 (mp) cc_final: 0.6163 (mp) REVERT: D 50 TRP cc_start: 0.7222 (p90) cc_final: 0.6338 (p90) REVERT: D 82 PHE cc_start: 0.7830 (m-80) cc_final: 0.7434 (m-10) REVERT: K 103 LYS cc_start: 0.6472 (tttt) cc_final: 0.6236 (mmtm) outliers start: 9 outliers final: 5 residues processed: 636 average time/residue: 0.1973 time to fit residues: 195.0801 Evaluate side-chains 336 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN A1084 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 637 ASN H 68 GLN E 812 ASN E1084 GLN E1129 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN J 637 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN F 637 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.083715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.064114 restraints weight = 202122.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.065052 restraints weight = 169150.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.065977 restraints weight = 141633.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.066710 restraints weight = 120118.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.066991 restraints weight = 108346.005| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29433 Z= 0.210 Angle : 0.824 11.806 40143 Z= 0.435 Chirality : 0.049 0.303 4647 Planarity : 0.006 0.057 5061 Dihedral : 9.552 80.536 5487 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.78 % Favored : 95.96 % Rotamer: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3543 helix: 0.63 (0.19), residues: 687 sheet: 0.09 (0.17), residues: 867 loop : 0.07 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 822 TYR 0.044 0.003 TYR E 909 PHE 0.024 0.003 PHE I1012 TRP 0.042 0.003 TRP H 50 HIS 0.008 0.001 HIS F 681 Details of bonding type rmsd covalent geometry : bond 0.00440 (29313) covalent geometry : angle 0.79308 (39825) SS BOND : bond 0.00594 ( 42) SS BOND : angle 1.20631 ( 84) hydrogen bonds : bond 0.06572 ( 1154) hydrogen bonds : angle 6.22445 ( 3024) link_ALPHA1-3 : bond 0.00500 ( 3) link_ALPHA1-3 : angle 1.70126 ( 9) link_ALPHA1-6 : bond 0.00019 ( 3) link_ALPHA1-6 : angle 1.64711 ( 9) link_BETA1-4 : bond 0.00537 ( 30) link_BETA1-4 : angle 2.20311 ( 90) link_NAG-ASN : bond 0.00377 ( 42) link_NAG-ASN : angle 3.56128 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 417 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5923 (mmt) cc_final: 0.4671 (mmt) REVERT: A 808 GLN cc_start: 0.9161 (tp40) cc_final: 0.8733 (tp-100) REVERT: A 819 GLN cc_start: 0.9136 (mt0) cc_final: 0.8927 (mm110) REVERT: A 900 ILE cc_start: 0.4884 (pt) cc_final: 0.4663 (pt) REVERT: A 906 MET cc_start: 0.1080 (ttm) cc_final: 0.0566 (tmm) REVERT: A 943 MET cc_start: 0.8339 (tpp) cc_final: 0.7957 (tpt) REVERT: A 1027 ASN cc_start: 0.8141 (m-40) cc_final: 0.7791 (m-40) REVERT: A 1074 ARG cc_start: 0.7443 (mmt90) cc_final: 0.6632 (tpp-160) REVERT: A 1090 GLU cc_start: 0.7794 (mm-30) cc_final: 0.6993 (pp20) REVERT: A 1101 ASP cc_start: 0.8732 (m-30) cc_final: 0.8484 (t0) REVERT: A 1102 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8267 (mmtt) REVERT: B 156 PHE cc_start: 0.8065 (m-80) cc_final: 0.7508 (m-80) REVERT: B 172 LEU cc_start: 0.7952 (tp) cc_final: 0.7681 (tp) REVERT: B 183 PHE cc_start: 0.8398 (p90) cc_final: 0.8143 (p90) REVERT: B 243 TYR cc_start: 0.7994 (m-80) cc_final: 0.7290 (m-80) REVERT: B 293 TYR cc_start: 0.7318 (p90) cc_final: 0.6925 (p90) REVERT: B 354 PHE cc_start: 0.5636 (p90) cc_final: 0.5337 (p90) REVERT: B 652 ARG cc_start: 0.6331 (tpt170) cc_final: 0.6003 (tpt170) REVERT: B 674 PHE cc_start: 0.8449 (m-80) cc_final: 0.8040 (m-80) REVERT: H 80 MET cc_start: 0.3874 (ttm) cc_final: 0.2696 (ttm) REVERT: E 757 MET cc_start: 0.5959 (mmt) cc_final: 0.4832 (mmt) REVERT: E 788 PHE cc_start: 0.7304 (m-80) cc_final: 0.6746 (m-80) REVERT: E 808 GLN cc_start: 0.9237 (tp40) cc_final: 0.8772 (tp-100) REVERT: E 900 ILE cc_start: 0.5184 (pt) cc_final: 0.4964 (pt) REVERT: E 906 MET cc_start: 0.0921 (ttm) cc_final: 0.0198 (tmm) REVERT: E 943 MET cc_start: 0.8066 (tpp) cc_final: 0.7762 (tpt) REVERT: E 1027 ASN cc_start: 0.8089 (m-40) cc_final: 0.7800 (m-40) REVERT: E 1090 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7048 (pp20) REVERT: E 1101 ASP cc_start: 0.8654 (m-30) cc_final: 0.8443 (t0) REVERT: E 1102 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8275 (mmtt) REVERT: E 1123 ILE cc_start: 0.8729 (tp) cc_final: 0.8321 (tt) REVERT: J 69 ILE cc_start: 0.6064 (tp) cc_final: 0.5658 (tp) REVERT: J 156 PHE cc_start: 0.7981 (m-80) cc_final: 0.7475 (m-80) REVERT: J 172 LEU cc_start: 0.7832 (tp) cc_final: 0.7489 (tp) REVERT: J 183 PHE cc_start: 0.8494 (p90) cc_final: 0.8104 (p90) REVERT: J 243 TYR cc_start: 0.7962 (m-80) cc_final: 0.7219 (m-80) REVERT: J 293 TYR cc_start: 0.7263 (p90) cc_final: 0.6686 (p90) REVERT: J 632 TYR cc_start: 0.8344 (m-80) cc_final: 0.8081 (m-80) REVERT: J 652 ARG cc_start: 0.6251 (tpt170) cc_final: 0.5968 (tpt170) REVERT: J 674 PHE cc_start: 0.8381 (m-80) cc_final: 0.7974 (m-80) REVERT: C 36 TRP cc_start: 0.5749 (m100) cc_final: 0.5437 (m-10) REVERT: C 58 GLU cc_start: 0.8290 (tp30) cc_final: 0.7917 (tp30) REVERT: C 80 MET cc_start: 0.3674 (ttm) cc_final: 0.2671 (ttm) REVERT: C 82 PHE cc_start: 0.8702 (m-80) cc_final: 0.7999 (m-10) REVERT: G 47 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5675 (mt) REVERT: I 757 MET cc_start: 0.6288 (mtt) cc_final: 0.5654 (mmt) REVERT: I 863 PRO cc_start: 0.7597 (Cg_exo) cc_final: 0.7391 (Cg_endo) REVERT: I 893 LEU cc_start: 0.8531 (mt) cc_final: 0.8250 (mt) REVERT: I 900 ILE cc_start: 0.4708 (pt) cc_final: 0.4490 (pt) REVERT: I 906 MET cc_start: 0.1376 (ttm) cc_final: 0.0931 (tmm) REVERT: I 943 MET cc_start: 0.8087 (tpp) cc_final: 0.7828 (tpt) REVERT: I 1027 ASN cc_start: 0.7824 (m-40) cc_final: 0.7469 (m-40) REVERT: I 1090 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6870 (pp20) REVERT: I 1101 ASP cc_start: 0.8630 (m-30) cc_final: 0.8404 (t0) REVERT: I 1102 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8303 (mmtt) REVERT: F 69 ILE cc_start: 0.6377 (tp) cc_final: 0.5903 (tp) REVERT: F 116 PHE cc_start: 0.6628 (p90) cc_final: 0.6349 (p90) REVERT: F 156 PHE cc_start: 0.7456 (m-10) cc_final: 0.7081 (m-10) REVERT: F 172 LEU cc_start: 0.8105 (tp) cc_final: 0.7831 (tp) REVERT: F 183 PHE cc_start: 0.8421 (p90) cc_final: 0.8079 (p90) REVERT: F 243 TYR cc_start: 0.7766 (m-80) cc_final: 0.7150 (m-80) REVERT: F 278 MET cc_start: 0.4926 (mmm) cc_final: 0.2781 (mmm) REVERT: F 293 TYR cc_start: 0.7098 (p90) cc_final: 0.6494 (p90) REVERT: F 351 TYR cc_start: 0.7399 (m-10) cc_final: 0.7004 (m-10) REVERT: F 354 PHE cc_start: 0.5151 (p90) cc_final: 0.4875 (p90) REVERT: F 652 ARG cc_start: 0.6454 (tpt170) cc_final: 0.6200 (tpt170) REVERT: F 674 PHE cc_start: 0.8519 (m-80) cc_final: 0.8096 (m-80) REVERT: D 18 VAL cc_start: 0.9521 (p) cc_final: 0.9248 (p) REVERT: D 36 TRP cc_start: 0.5478 (m100) cc_final: 0.4922 (m-10) REVERT: D 80 MET cc_start: 0.4630 (ttm) cc_final: 0.3762 (ttm) REVERT: D 82 PHE cc_start: 0.8552 (m-80) cc_final: 0.7949 (m-10) outliers start: 8 outliers final: 1 residues processed: 425 average time/residue: 0.1878 time to fit residues: 127.0814 Evaluate side-chains 301 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 246 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 339 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 161 optimal weight: 0.0030 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1129 ASN A1132 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 346 GLN H 68 GLN E 808 GLN E 833 GLN E1084 GLN E1132 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 ASN ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 833 GLN I1066 GLN I1084 GLN I1129 ASN I1132 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1163 ASN ** I1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.081090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.061970 restraints weight = 208824.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.063028 restraints weight = 175284.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.063668 restraints weight = 146906.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.064192 restraints weight = 128188.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.064724 restraints weight = 116379.484| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29433 Z= 0.205 Angle : 0.766 10.961 40143 Z= 0.396 Chirality : 0.047 0.371 4647 Planarity : 0.005 0.059 5061 Dihedral : 8.065 62.537 5487 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.23 % Favored : 95.43 % Rotamer: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3543 helix: 0.08 (0.18), residues: 681 sheet: -0.20 (0.17), residues: 762 loop : -0.30 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1069 TYR 0.036 0.002 TYR I 909 PHE 0.021 0.003 PHE I1012 TRP 0.050 0.004 TRP H 50 HIS 0.007 0.002 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00426 (29313) covalent geometry : angle 0.74617 (39825) SS BOND : bond 0.00479 ( 42) SS BOND : angle 0.99671 ( 84) hydrogen bonds : bond 0.05637 ( 1154) hydrogen bonds : angle 6.22467 ( 3024) link_ALPHA1-3 : bond 0.01218 ( 3) link_ALPHA1-3 : angle 1.81506 ( 9) link_ALPHA1-6 : bond 0.00299 ( 3) link_ALPHA1-6 : angle 1.41852 ( 9) link_BETA1-4 : bond 0.00501 ( 30) link_BETA1-4 : angle 1.91144 ( 90) link_NAG-ASN : bond 0.00431 ( 42) link_NAG-ASN : angle 2.66924 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 362 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5789 (mmt) cc_final: 0.4726 (mmt) REVERT: A 808 GLN cc_start: 0.9148 (tp40) cc_final: 0.8936 (tm-30) REVERT: A 906 MET cc_start: 0.1322 (ttm) cc_final: 0.0605 (tmm) REVERT: A 943 MET cc_start: 0.8312 (tpp) cc_final: 0.7949 (tpt) REVERT: A 1027 ASN cc_start: 0.8303 (m-40) cc_final: 0.7867 (m-40) REVERT: A 1074 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7205 (tpm170) REVERT: A 1090 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7047 (pp20) REVERT: B 69 ILE cc_start: 0.6602 (tp) cc_final: 0.6194 (tp) REVERT: B 156 PHE cc_start: 0.8182 (m-80) cc_final: 0.7688 (m-80) REVERT: B 172 LEU cc_start: 0.7856 (tp) cc_final: 0.7560 (tp) REVERT: B 180 LEU cc_start: 0.8922 (tt) cc_final: 0.8591 (mt) REVERT: B 183 PHE cc_start: 0.8471 (p90) cc_final: 0.8170 (p90) REVERT: B 187 LEU cc_start: 0.8001 (pt) cc_final: 0.7623 (pt) REVERT: B 243 TYR cc_start: 0.7807 (m-80) cc_final: 0.7460 (m-80) REVERT: B 293 TYR cc_start: 0.7241 (p90) cc_final: 0.6510 (p90) REVERT: H 80 MET cc_start: 0.5127 (ttm) cc_final: 0.4562 (ttm) REVERT: H 82 PHE cc_start: 0.9003 (m-80) cc_final: 0.8802 (m-10) REVERT: E 757 MET cc_start: 0.5854 (mmt) cc_final: 0.5634 (tpt) REVERT: E 808 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8859 (tp-100) REVERT: E 893 LEU cc_start: 0.8845 (mt) cc_final: 0.8233 (mt) REVERT: E 906 MET cc_start: 0.0731 (ttm) cc_final: 0.0336 (tmm) REVERT: E 943 MET cc_start: 0.8019 (tpp) cc_final: 0.7683 (tpt) REVERT: E 1027 ASN cc_start: 0.8258 (m-40) cc_final: 0.7806 (m-40) REVERT: E 1090 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7026 (pp20) REVERT: J 69 ILE cc_start: 0.6787 (tp) cc_final: 0.6316 (tp) REVERT: J 116 PHE cc_start: 0.6622 (p90) cc_final: 0.6297 (p90) REVERT: J 172 LEU cc_start: 0.7901 (tp) cc_final: 0.7609 (tp) REVERT: J 183 PHE cc_start: 0.8542 (p90) cc_final: 0.8275 (p90) REVERT: J 187 LEU cc_start: 0.7896 (pt) cc_final: 0.7583 (pt) REVERT: J 243 TYR cc_start: 0.7895 (m-80) cc_final: 0.7334 (m-80) REVERT: J 293 TYR cc_start: 0.7477 (p90) cc_final: 0.6698 (p90) REVERT: J 674 PHE cc_start: 0.8549 (m-80) cc_final: 0.8339 (m-80) REVERT: C 82 PHE cc_start: 0.8997 (m-80) cc_final: 0.8433 (m-10) REVERT: I 757 MET cc_start: 0.6352 (mtt) cc_final: 0.6092 (mtt) REVERT: I 848 ASN cc_start: 0.8765 (m-40) cc_final: 0.8560 (m-40) REVERT: I 893 LEU cc_start: 0.8386 (mt) cc_final: 0.7993 (mt) REVERT: I 906 MET cc_start: 0.1094 (ttm) cc_final: 0.0706 (tmm) REVERT: I 943 MET cc_start: 0.8197 (tpp) cc_final: 0.7847 (tpt) REVERT: I 1027 ASN cc_start: 0.8004 (m-40) cc_final: 0.7511 (m-40) REVERT: I 1090 GLU cc_start: 0.7961 (mm-30) cc_final: 0.6959 (pp20) REVERT: I 1123 ILE cc_start: 0.9050 (tp) cc_final: 0.8784 (tp) REVERT: F 108 ASP cc_start: 0.6457 (m-30) cc_final: 0.6141 (m-30) REVERT: F 172 LEU cc_start: 0.7918 (tp) cc_final: 0.7645 (tp) REVERT: F 183 PHE cc_start: 0.8479 (p90) cc_final: 0.8220 (p90) REVERT: F 187 LEU cc_start: 0.7922 (pt) cc_final: 0.7575 (pt) REVERT: F 243 TYR cc_start: 0.7776 (m-80) cc_final: 0.7160 (m-80) REVERT: F 266 PHE cc_start: 0.8810 (m-80) cc_final: 0.8293 (m-80) REVERT: F 278 MET cc_start: 0.5366 (mmm) cc_final: 0.2871 (mmm) REVERT: F 293 TYR cc_start: 0.7349 (p90) cc_final: 0.6491 (p90) REVERT: F 674 PHE cc_start: 0.8503 (m-80) cc_final: 0.8279 (m-80) REVERT: F 696 MET cc_start: 0.2459 (ptt) cc_final: 0.2001 (ptt) REVERT: D 18 VAL cc_start: 0.9581 (p) cc_final: 0.9269 (p) REVERT: D 36 TRP cc_start: 0.5675 (m100) cc_final: 0.5113 (m-10) REVERT: D 59 TYR cc_start: 0.6252 (p90) cc_final: 0.5667 (p90) REVERT: D 80 MET cc_start: 0.5100 (ttm) cc_final: 0.3997 (ttm) REVERT: D 82 PHE cc_start: 0.8942 (m-80) cc_final: 0.8290 (m-10) REVERT: K 47 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.5991 (mt) outliers start: 5 outliers final: 0 residues processed: 366 average time/residue: 0.1904 time to fit residues: 110.3598 Evaluate side-chains 262 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 177 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN A 792 GLN A 800 GLN A 808 GLN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN E 772 GLN E 792 GLN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1084 GLN E1163 ASN J 277 ASN J 346 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1169 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 346 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.078637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.060580 restraints weight = 215402.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.060951 restraints weight = 190542.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.061593 restraints weight = 162453.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.062787 restraints weight = 142613.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.062824 restraints weight = 120904.935| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29433 Z= 0.237 Angle : 0.805 14.964 40143 Z= 0.414 Chirality : 0.049 0.458 4647 Planarity : 0.006 0.052 5061 Dihedral : 7.725 58.858 5487 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.97 % Favored : 94.69 % Rotamer: Outliers : 0.30 % Allowed : 2.77 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 3543 helix: -0.59 (0.18), residues: 681 sheet: -0.46 (0.17), residues: 780 loop : -0.76 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 62 TYR 0.037 0.003 TYR F 64 PHE 0.026 0.003 PHE E1012 TRP 0.041 0.003 TRP C 36 HIS 0.008 0.002 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00491 (29313) covalent geometry : angle 0.78924 (39825) SS BOND : bond 0.00552 ( 42) SS BOND : angle 1.13154 ( 84) hydrogen bonds : bond 0.05620 ( 1154) hydrogen bonds : angle 6.53316 ( 3024) link_ALPHA1-3 : bond 0.01379 ( 3) link_ALPHA1-3 : angle 2.01806 ( 9) link_ALPHA1-6 : bond 0.00269 ( 3) link_ALPHA1-6 : angle 1.54889 ( 9) link_BETA1-4 : bond 0.00387 ( 30) link_BETA1-4 : angle 1.86390 ( 90) link_NAG-ASN : bond 0.00567 ( 42) link_NAG-ASN : angle 2.43462 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 329 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5959 (mmt) cc_final: 0.5456 (tpp) REVERT: A 893 LEU cc_start: 0.8721 (mt) cc_final: 0.8143 (mt) REVERT: A 906 MET cc_start: 0.1805 (ttm) cc_final: 0.1062 (tmm) REVERT: A 943 MET cc_start: 0.8211 (tpp) cc_final: 0.7998 (tpp) REVERT: A 955 ILE cc_start: 0.6057 (mt) cc_final: 0.5772 (mm) REVERT: A 1026 VAL cc_start: 0.8588 (t) cc_final: 0.8214 (t) REVERT: A 1027 ASN cc_start: 0.8196 (m-40) cc_final: 0.6957 (p0) REVERT: A 1028 ASN cc_start: 0.9081 (t0) cc_final: 0.8867 (t0) REVERT: A 1074 ARG cc_start: 0.7533 (mmt90) cc_final: 0.7276 (tpm170) REVERT: A 1090 GLU cc_start: 0.8069 (mm-30) cc_final: 0.6844 (pp20) REVERT: B 172 LEU cc_start: 0.7965 (tp) cc_final: 0.7634 (tp) REVERT: B 180 LEU cc_start: 0.8896 (tt) cc_final: 0.8587 (mt) REVERT: B 183 PHE cc_start: 0.8542 (p90) cc_final: 0.8234 (p90) REVERT: B 243 TYR cc_start: 0.7821 (m-80) cc_final: 0.7411 (m-80) REVERT: B 278 MET cc_start: 0.5932 (tpp) cc_final: 0.3831 (ttm) REVERT: B 293 TYR cc_start: 0.7435 (p90) cc_final: 0.6672 (p90) REVERT: B 686 MET cc_start: 0.5071 (mmp) cc_final: 0.4807 (mmm) REVERT: B 689 TYR cc_start: 0.8162 (p90) cc_final: 0.7961 (p90) REVERT: H 82 PHE cc_start: 0.9219 (m-80) cc_final: 0.8722 (m-10) REVERT: E 757 MET cc_start: 0.6240 (mmt) cc_final: 0.5976 (tpt) REVERT: E 893 LEU cc_start: 0.8479 (mt) cc_final: 0.8073 (mt) REVERT: E 906 MET cc_start: 0.1200 (ttm) cc_final: 0.0748 (tmm) REVERT: E 943 MET cc_start: 0.8101 (tpp) cc_final: 0.7688 (tpt) REVERT: E 955 ILE cc_start: 0.5964 (mt) cc_final: 0.5711 (mm) REVERT: E 1021 LYS cc_start: 0.9266 (mmmt) cc_final: 0.9017 (mmtt) REVERT: E 1027 ASN cc_start: 0.8219 (m-40) cc_final: 0.6886 (p0) REVERT: E 1028 ASN cc_start: 0.9005 (t0) cc_final: 0.8763 (t0) REVERT: E 1074 ARG cc_start: 0.7511 (mmt90) cc_final: 0.7228 (tpm170) REVERT: E 1090 GLU cc_start: 0.8136 (mm-30) cc_final: 0.6924 (pp20) REVERT: J 116 PHE cc_start: 0.7047 (p90) cc_final: 0.6641 (p90) REVERT: J 172 LEU cc_start: 0.8056 (tp) cc_final: 0.7788 (tp) REVERT: J 183 PHE cc_start: 0.8659 (p90) cc_final: 0.8376 (p90) REVERT: J 243 TYR cc_start: 0.7989 (m-80) cc_final: 0.7306 (m-80) REVERT: J 293 TYR cc_start: 0.7528 (p90) cc_final: 0.7080 (p90) REVERT: J 686 MET cc_start: 0.4906 (mmp) cc_final: 0.4646 (mmm) REVERT: J 696 MET cc_start: 0.2337 (ptt) cc_final: 0.1822 (ptt) REVERT: C 80 MET cc_start: 0.6198 (ttm) cc_final: 0.5082 (ttm) REVERT: C 82 PHE cc_start: 0.9352 (m-80) cc_final: 0.9081 (m-10) REVERT: I 757 MET cc_start: 0.6697 (mtt) cc_final: 0.6171 (mtt) REVERT: I 893 LEU cc_start: 0.8438 (mt) cc_final: 0.8047 (mt) REVERT: I 897 LYS cc_start: 0.7618 (mppt) cc_final: 0.7407 (mmtm) REVERT: I 906 MET cc_start: 0.1145 (ttm) cc_final: 0.0708 (tmm) REVERT: I 943 MET cc_start: 0.8273 (tpp) cc_final: 0.7855 (tpt) REVERT: I 955 ILE cc_start: 0.6305 (mt) cc_final: 0.6030 (mm) REVERT: I 1026 VAL cc_start: 0.8454 (t) cc_final: 0.8078 (t) REVERT: I 1027 ASN cc_start: 0.8220 (m-40) cc_final: 0.6815 (p0) REVERT: I 1090 GLU cc_start: 0.8215 (mm-30) cc_final: 0.6857 (pp20) REVERT: F 108 ASP cc_start: 0.6127 (m-30) cc_final: 0.5846 (m-30) REVERT: F 172 LEU cc_start: 0.8045 (tp) cc_final: 0.7797 (tp) REVERT: F 183 PHE cc_start: 0.8595 (p90) cc_final: 0.8378 (p90) REVERT: F 243 TYR cc_start: 0.7813 (m-80) cc_final: 0.7239 (m-80) REVERT: F 266 PHE cc_start: 0.8794 (m-80) cc_final: 0.8368 (m-80) REVERT: F 278 MET cc_start: 0.5592 (mmm) cc_final: 0.2822 (mmm) REVERT: F 293 TYR cc_start: 0.7625 (p90) cc_final: 0.7254 (p90) REVERT: F 327 PHE cc_start: 0.7928 (m-80) cc_final: 0.7592 (m-80) REVERT: F 686 MET cc_start: 0.5150 (mmp) cc_final: 0.4940 (mmm) REVERT: F 689 TYR cc_start: 0.8211 (p90) cc_final: 0.8005 (p90) REVERT: F 696 MET cc_start: 0.2572 (ptt) cc_final: 0.2196 (ptt) REVERT: D 18 VAL cc_start: 0.9617 (p) cc_final: 0.9354 (p) REVERT: D 36 TRP cc_start: 0.5834 (m100) cc_final: 0.5511 (m-10) REVERT: D 80 MET cc_start: 0.5608 (ttm) cc_final: 0.4383 (ttm) REVERT: D 82 PHE cc_start: 0.9184 (m-80) cc_final: 0.8610 (m-10) outliers start: 9 outliers final: 1 residues processed: 338 average time/residue: 0.1689 time to fit residues: 91.9181 Evaluate side-chains 248 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 89 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 348 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN A 987 GLN A1066 GLN A1084 GLN H 68 GLN H 81 GLN ** E 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1066 GLN E1084 GLN E1163 ASN J 346 GLN J 628 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 792 GLN I 808 GLN ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN I1129 ASN F 346 GLN ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.078985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.060817 restraints weight = 214542.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.061591 restraints weight = 185567.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.062320 restraints weight = 154122.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.062697 restraints weight = 136228.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.063236 restraints weight = 123701.707| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29433 Z= 0.184 Angle : 0.726 11.277 40143 Z= 0.370 Chirality : 0.047 0.465 4647 Planarity : 0.005 0.048 5061 Dihedral : 7.328 58.229 5487 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.11 % Favored : 94.55 % Rotamer: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3543 helix: -0.33 (0.18), residues: 666 sheet: -0.62 (0.17), residues: 816 loop : -0.87 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1069 TYR 0.030 0.002 TYR I 909 PHE 0.053 0.002 PHE I 850 TRP 0.052 0.003 TRP H 50 HIS 0.006 0.001 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00384 (29313) covalent geometry : angle 0.70398 (39825) SS BOND : bond 0.00493 ( 42) SS BOND : angle 1.01381 ( 84) hydrogen bonds : bond 0.05014 ( 1154) hydrogen bonds : angle 6.35260 ( 3024) link_ALPHA1-3 : bond 0.01617 ( 3) link_ALPHA1-3 : angle 1.80102 ( 9) link_ALPHA1-6 : bond 0.00529 ( 3) link_ALPHA1-6 : angle 1.33693 ( 9) link_BETA1-4 : bond 0.00387 ( 30) link_BETA1-4 : angle 1.80589 ( 90) link_NAG-ASN : bond 0.00432 ( 42) link_NAG-ASN : angle 2.79567 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5960 (mmt) cc_final: 0.5463 (tpp) REVERT: A 833 GLN cc_start: 0.7001 (tp-100) cc_final: 0.6768 (tp40) REVERT: A 906 MET cc_start: 0.1624 (ttm) cc_final: 0.0909 (tmm) REVERT: A 913 MET cc_start: 0.8180 (mpp) cc_final: 0.7537 (mpp) REVERT: A 921 ARG cc_start: 0.5277 (ttm170) cc_final: 0.3180 (pmt-80) REVERT: A 955 ILE cc_start: 0.5975 (mt) cc_final: 0.5551 (mm) REVERT: A 1026 VAL cc_start: 0.8625 (t) cc_final: 0.8238 (t) REVERT: A 1027 ASN cc_start: 0.8190 (m-40) cc_final: 0.6875 (p0) REVERT: A 1028 ASN cc_start: 0.9074 (t0) cc_final: 0.8743 (t0) REVERT: A 1090 GLU cc_start: 0.8128 (mm-30) cc_final: 0.6976 (pp20) REVERT: A 1102 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8672 (mmpt) REVERT: B 108 ASP cc_start: 0.6278 (m-30) cc_final: 0.5977 (m-30) REVERT: B 156 PHE cc_start: 0.8068 (m-10) cc_final: 0.7628 (m-80) REVERT: B 172 LEU cc_start: 0.7899 (tp) cc_final: 0.7571 (tp) REVERT: B 180 LEU cc_start: 0.8892 (tt) cc_final: 0.8614 (mt) REVERT: B 183 PHE cc_start: 0.8529 (p90) cc_final: 0.8193 (p90) REVERT: B 228 PHE cc_start: 0.9329 (t80) cc_final: 0.8982 (t80) REVERT: B 243 TYR cc_start: 0.7902 (m-80) cc_final: 0.7482 (m-80) REVERT: B 278 MET cc_start: 0.5853 (tpp) cc_final: 0.4534 (ttm) REVERT: B 293 TYR cc_start: 0.7251 (p90) cc_final: 0.6612 (p90) REVERT: B 327 PHE cc_start: 0.8123 (m-80) cc_final: 0.7804 (m-80) REVERT: E 757 MET cc_start: 0.6312 (mmt) cc_final: 0.6077 (tpt) REVERT: E 906 MET cc_start: 0.0978 (ttm) cc_final: 0.0521 (tmm) REVERT: E 913 MET cc_start: 0.7976 (mpp) cc_final: 0.7349 (mpp) REVERT: E 943 MET cc_start: 0.8205 (tpp) cc_final: 0.7752 (tpt) REVERT: E 955 ILE cc_start: 0.6118 (mt) cc_final: 0.5705 (mm) REVERT: E 1021 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9050 (mmtt) REVERT: E 1027 ASN cc_start: 0.8260 (m-40) cc_final: 0.6784 (p0) REVERT: E 1028 ASN cc_start: 0.8980 (t0) cc_final: 0.8671 (t0) REVERT: E 1090 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7012 (pp20) REVERT: J 108 ASP cc_start: 0.6298 (m-30) cc_final: 0.5790 (m-30) REVERT: J 116 PHE cc_start: 0.6984 (p90) cc_final: 0.6659 (p90) REVERT: J 172 LEU cc_start: 0.7965 (tp) cc_final: 0.7633 (tp) REVERT: J 183 PHE cc_start: 0.8667 (p90) cc_final: 0.8355 (p90) REVERT: J 243 TYR cc_start: 0.7946 (m-80) cc_final: 0.7445 (m-80) REVERT: J 293 TYR cc_start: 0.7442 (p90) cc_final: 0.6936 (p90) REVERT: J 327 PHE cc_start: 0.8309 (m-80) cc_final: 0.8045 (m-80) REVERT: J 632 TYR cc_start: 0.8752 (m-80) cc_final: 0.8527 (m-80) REVERT: J 686 MET cc_start: 0.5225 (mmp) cc_final: 0.4749 (mmm) REVERT: J 696 MET cc_start: 0.2333 (ptt) cc_final: 0.1841 (ptt) REVERT: C 80 MET cc_start: 0.5738 (ttm) cc_final: 0.3756 (ttm) REVERT: I 757 MET cc_start: 0.6480 (mtt) cc_final: 0.6104 (mtt) REVERT: I 893 LEU cc_start: 0.8666 (mt) cc_final: 0.8276 (mt) REVERT: I 906 MET cc_start: 0.0847 (ttm) cc_final: 0.0557 (tmm) REVERT: I 943 MET cc_start: 0.8231 (tpp) cc_final: 0.7755 (tpt) REVERT: I 955 ILE cc_start: 0.6147 (mt) cc_final: 0.5725 (mm) REVERT: I 1021 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8653 (mmtm) REVERT: I 1090 GLU cc_start: 0.8254 (mm-30) cc_final: 0.6929 (pp20) REVERT: F 108 ASP cc_start: 0.6082 (m-30) cc_final: 0.5660 (m-30) REVERT: F 172 LEU cc_start: 0.8020 (tp) cc_final: 0.7704 (tp) REVERT: F 180 LEU cc_start: 0.9062 (tt) cc_final: 0.8761 (mt) REVERT: F 183 PHE cc_start: 0.8584 (p90) cc_final: 0.8325 (p90) REVERT: F 243 TYR cc_start: 0.7870 (m-80) cc_final: 0.7449 (m-80) REVERT: F 254 PHE cc_start: 0.6237 (t80) cc_final: 0.5880 (t80) REVERT: F 266 PHE cc_start: 0.8828 (m-80) cc_final: 0.8429 (m-80) REVERT: F 278 MET cc_start: 0.5289 (mmm) cc_final: 0.2803 (mmm) REVERT: F 293 TYR cc_start: 0.7541 (p90) cc_final: 0.6913 (p90) REVERT: F 327 PHE cc_start: 0.8149 (m-80) cc_final: 0.7794 (m-80) REVERT: F 674 PHE cc_start: 0.8546 (m-80) cc_final: 0.8304 (m-10) REVERT: F 689 TYR cc_start: 0.8175 (p90) cc_final: 0.7918 (p90) REVERT: F 696 MET cc_start: 0.2375 (ptt) cc_final: 0.1975 (ptt) REVERT: D 18 VAL cc_start: 0.9564 (p) cc_final: 0.9250 (p) REVERT: D 36 TRP cc_start: 0.5783 (m100) cc_final: 0.5506 (m-10) REVERT: D 59 TYR cc_start: 0.6742 (p90) cc_final: 0.6446 (p90) REVERT: D 80 MET cc_start: 0.5480 (ttm) cc_final: 0.4268 (ttm) REVERT: D 82 PHE cc_start: 0.9115 (m-80) cc_final: 0.8524 (m-10) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.1747 time to fit residues: 92.4696 Evaluate side-chains 253 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 221 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 147 optimal weight: 0.3980 chunk 165 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 251 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 GLN ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN L 90 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN F 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.079756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.061247 restraints weight = 213496.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.062511 restraints weight = 181923.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.063037 restraints weight = 148586.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.063413 restraints weight = 131716.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.063988 restraints weight = 122089.964| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29433 Z= 0.144 Angle : 0.670 9.960 40143 Z= 0.342 Chirality : 0.046 0.454 4647 Planarity : 0.005 0.045 5061 Dihedral : 6.767 57.298 5487 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.33 % Favored : 94.41 % Rotamer: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3543 helix: -0.06 (0.19), residues: 687 sheet: -0.57 (0.18), residues: 798 loop : -0.88 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 979 TYR 0.024 0.002 TYR I 909 PHE 0.024 0.002 PHE F 281 TRP 0.039 0.003 TRP D 50 HIS 0.003 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00304 (29313) covalent geometry : angle 0.64794 (39825) SS BOND : bond 0.00351 ( 42) SS BOND : angle 0.91961 ( 84) hydrogen bonds : bond 0.04553 ( 1154) hydrogen bonds : angle 6.12466 ( 3024) link_ALPHA1-3 : bond 0.01687 ( 3) link_ALPHA1-3 : angle 1.73861 ( 9) link_ALPHA1-6 : bond 0.00734 ( 3) link_ALPHA1-6 : angle 1.24323 ( 9) link_BETA1-4 : bond 0.00402 ( 30) link_BETA1-4 : angle 1.78398 ( 90) link_NAG-ASN : bond 0.00325 ( 42) link_NAG-ASN : angle 2.63955 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5985 (mmt) cc_final: 0.5521 (tpp) REVERT: A 833 GLN cc_start: 0.7012 (tp-100) cc_final: 0.6798 (tp40) REVERT: A 906 MET cc_start: 0.1442 (ttm) cc_final: 0.1001 (tmm) REVERT: A 913 MET cc_start: 0.8377 (mpp) cc_final: 0.7797 (mpp) REVERT: A 921 ARG cc_start: 0.5378 (ttm170) cc_final: 0.3840 (pmt-80) REVERT: A 943 MET cc_start: 0.7821 (tpp) cc_final: 0.7423 (tpt) REVERT: A 955 ILE cc_start: 0.6035 (mt) cc_final: 0.5642 (mm) REVERT: A 1021 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8488 (mmtm) REVERT: A 1027 ASN cc_start: 0.8238 (m-40) cc_final: 0.6929 (p0) REVERT: A 1028 ASN cc_start: 0.8961 (t0) cc_final: 0.8728 (t0) REVERT: A 1090 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7226 (pp20) REVERT: A 1102 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8673 (mmpt) REVERT: B 27 LYS cc_start: 0.8129 (mppt) cc_final: 0.7799 (mmmt) REVERT: B 108 ASP cc_start: 0.6178 (m-30) cc_final: 0.5837 (m-30) REVERT: B 116 PHE cc_start: 0.7002 (p90) cc_final: 0.6715 (p90) REVERT: B 156 PHE cc_start: 0.8026 (m-10) cc_final: 0.7518 (m-80) REVERT: B 172 LEU cc_start: 0.7916 (tp) cc_final: 0.7592 (tp) REVERT: B 180 LEU cc_start: 0.8877 (tt) cc_final: 0.8600 (mt) REVERT: B 183 PHE cc_start: 0.8486 (p90) cc_final: 0.8084 (p90) REVERT: B 228 PHE cc_start: 0.9362 (t80) cc_final: 0.9016 (t80) REVERT: B 243 TYR cc_start: 0.7897 (m-80) cc_final: 0.7489 (m-80) REVERT: B 266 PHE cc_start: 0.9123 (m-10) cc_final: 0.8653 (m-80) REVERT: B 278 MET cc_start: 0.6084 (tpp) cc_final: 0.4840 (ttm) REVERT: B 293 TYR cc_start: 0.7124 (p90) cc_final: 0.6544 (p90) REVERT: B 327 PHE cc_start: 0.8158 (m-80) cc_final: 0.7846 (m-80) REVERT: B 689 TYR cc_start: 0.8194 (p90) cc_final: 0.7940 (p90) REVERT: H 80 MET cc_start: 0.6434 (ttm) cc_final: 0.4378 (ttm) REVERT: E 757 MET cc_start: 0.6273 (mmt) cc_final: 0.5366 (tpt) REVERT: E 906 MET cc_start: 0.0924 (ttm) cc_final: 0.0452 (tmm) REVERT: E 913 MET cc_start: 0.8196 (mpp) cc_final: 0.7585 (mpp) REVERT: E 921 ARG cc_start: 0.4909 (ttm170) cc_final: 0.2981 (pmt-80) REVERT: E 943 MET cc_start: 0.8299 (tpp) cc_final: 0.8032 (tpt) REVERT: E 955 ILE cc_start: 0.6368 (mt) cc_final: 0.6027 (mm) REVERT: E 1027 ASN cc_start: 0.8107 (m-40) cc_final: 0.6647 (p0) REVERT: E 1028 ASN cc_start: 0.8867 (t0) cc_final: 0.8646 (t0) REVERT: E 1074 ARG cc_start: 0.7372 (mmt90) cc_final: 0.7128 (tpp-160) REVERT: E 1090 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7095 (pp20) REVERT: J 108 ASP cc_start: 0.6244 (m-30) cc_final: 0.5859 (m-30) REVERT: J 172 LEU cc_start: 0.7984 (tp) cc_final: 0.7655 (tp) REVERT: J 183 PHE cc_start: 0.8607 (p90) cc_final: 0.8267 (p90) REVERT: J 228 PHE cc_start: 0.9450 (t80) cc_final: 0.9219 (t80) REVERT: J 243 TYR cc_start: 0.7963 (m-80) cc_final: 0.7418 (m-80) REVERT: J 278 MET cc_start: 0.5387 (ttp) cc_final: 0.4633 (ttm) REVERT: J 293 TYR cc_start: 0.7416 (p90) cc_final: 0.6869 (p90) REVERT: J 327 PHE cc_start: 0.8336 (m-80) cc_final: 0.8027 (m-80) REVERT: J 632 TYR cc_start: 0.8710 (m-80) cc_final: 0.8462 (m-80) REVERT: J 686 MET cc_start: 0.4912 (mmp) cc_final: 0.4654 (mmm) REVERT: C 80 MET cc_start: 0.5580 (ttm) cc_final: 0.5285 (ttm) REVERT: I 913 MET cc_start: 0.7811 (mtm) cc_final: 0.7517 (mtm) REVERT: I 921 ARG cc_start: 0.5265 (ttm170) cc_final: 0.3183 (pmt-80) REVERT: I 943 MET cc_start: 0.8147 (tpp) cc_final: 0.7806 (tpp) REVERT: I 955 ILE cc_start: 0.6049 (mt) cc_final: 0.5775 (mm) REVERT: I 1021 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8559 (mmtm) REVERT: I 1090 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7042 (pp20) REVERT: F 108 ASP cc_start: 0.6123 (m-30) cc_final: 0.5640 (m-30) REVERT: F 172 LEU cc_start: 0.7996 (tp) cc_final: 0.7650 (tp) REVERT: F 180 LEU cc_start: 0.9063 (tt) cc_final: 0.8795 (mt) REVERT: F 183 PHE cc_start: 0.8573 (p90) cc_final: 0.8285 (p90) REVERT: F 243 TYR cc_start: 0.7912 (m-80) cc_final: 0.7491 (m-80) REVERT: F 254 PHE cc_start: 0.6695 (t80) cc_final: 0.6388 (t80) REVERT: F 266 PHE cc_start: 0.8769 (m-80) cc_final: 0.8280 (m-80) REVERT: F 278 MET cc_start: 0.5206 (mmm) cc_final: 0.3324 (mmm) REVERT: F 293 TYR cc_start: 0.7573 (p90) cc_final: 0.7153 (p90) REVERT: F 327 PHE cc_start: 0.8171 (m-80) cc_final: 0.7803 (m-80) REVERT: F 689 TYR cc_start: 0.8137 (p90) cc_final: 0.7884 (p90) REVERT: F 696 MET cc_start: 0.2443 (ptt) cc_final: 0.2018 (ptt) REVERT: D 18 VAL cc_start: 0.9546 (p) cc_final: 0.9305 (p) REVERT: D 80 MET cc_start: 0.5203 (ttm) cc_final: 0.4087 (ttm) REVERT: D 82 PHE cc_start: 0.9217 (m-80) cc_final: 0.8860 (m-10) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.1729 time to fit residues: 95.8569 Evaluate side-chains 255 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 219 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 318 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN H 68 GLN L 89 GLN E1163 ASN ** J 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1084 GLN I1132 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.077018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.059198 restraints weight = 223046.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.059959 restraints weight = 192203.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.060530 restraints weight = 165696.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.060845 restraints weight = 145840.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.061452 restraints weight = 133705.719| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 29433 Z= 0.238 Angle : 0.807 10.410 40143 Z= 0.413 Chirality : 0.050 0.645 4647 Planarity : 0.006 0.047 5061 Dihedral : 7.393 58.709 5487 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.77 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3543 helix: -0.62 (0.18), residues: 666 sheet: -0.72 (0.18), residues: 762 loop : -1.15 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1069 TYR 0.032 0.003 TYR I 909 PHE 0.039 0.003 PHE I1012 TRP 0.034 0.003 TRP H 36 HIS 0.008 0.002 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00497 (29313) covalent geometry : angle 0.78644 (39825) SS BOND : bond 0.00505 ( 42) SS BOND : angle 1.06070 ( 84) hydrogen bonds : bond 0.05403 ( 1154) hydrogen bonds : angle 6.71424 ( 3024) link_ALPHA1-3 : bond 0.01745 ( 3) link_ALPHA1-3 : angle 1.84840 ( 9) link_ALPHA1-6 : bond 0.00195 ( 3) link_ALPHA1-6 : angle 1.69342 ( 9) link_BETA1-4 : bond 0.00444 ( 30) link_BETA1-4 : angle 1.99826 ( 90) link_NAG-ASN : bond 0.00637 ( 42) link_NAG-ASN : angle 2.82616 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.6034 (mmt) cc_final: 0.5109 (tpp) REVERT: A 788 PHE cc_start: 0.7376 (m-80) cc_final: 0.7124 (m-80) REVERT: A 833 GLN cc_start: 0.7176 (tp-100) cc_final: 0.6923 (tp-100) REVERT: A 842 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: A 906 MET cc_start: 0.1568 (ttm) cc_final: 0.1134 (tmm) REVERT: A 913 MET cc_start: 0.8600 (mpp) cc_final: 0.7947 (mpp) REVERT: A 921 ARG cc_start: 0.5707 (ttm170) cc_final: 0.4039 (pmt-80) REVERT: A 943 MET cc_start: 0.7778 (tpp) cc_final: 0.7355 (tpt) REVERT: A 1102 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8509 (mmmt) REVERT: B 108 ASP cc_start: 0.6437 (m-30) cc_final: 0.6195 (m-30) REVERT: B 116 PHE cc_start: 0.7378 (p90) cc_final: 0.7116 (p90) REVERT: B 161 MET cc_start: 0.4436 (mmp) cc_final: 0.4173 (mmm) REVERT: B 172 LEU cc_start: 0.8125 (tp) cc_final: 0.7868 (tp) REVERT: B 183 PHE cc_start: 0.8479 (p90) cc_final: 0.8041 (p90) REVERT: B 228 PHE cc_start: 0.9324 (t80) cc_final: 0.9078 (t80) REVERT: B 243 TYR cc_start: 0.7892 (m-80) cc_final: 0.7369 (m-80) REVERT: B 278 MET cc_start: 0.6183 (tpp) cc_final: 0.5604 (ttm) REVERT: B 689 TYR cc_start: 0.8199 (p90) cc_final: 0.7988 (p90) REVERT: B 696 MET cc_start: 0.2633 (ptt) cc_final: 0.2206 (ptt) REVERT: H 80 MET cc_start: 0.6798 (ttm) cc_final: 0.6321 (ttm) REVERT: E 757 MET cc_start: 0.6404 (mmt) cc_final: 0.5554 (tpt) REVERT: E 906 MET cc_start: 0.1216 (ttm) cc_final: 0.0733 (tmm) REVERT: E 913 MET cc_start: 0.8482 (mpp) cc_final: 0.7828 (mpp) REVERT: E 943 MET cc_start: 0.8255 (tpp) cc_final: 0.7818 (tpt) REVERT: E 955 ILE cc_start: 0.6403 (mt) cc_final: 0.5840 (mm) REVERT: E 1021 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8528 (mmtm) REVERT: E 1074 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7255 (tpm170) REVERT: E 1090 GLU cc_start: 0.8230 (mm-30) cc_final: 0.6833 (pp20) REVERT: E 1102 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8540 (mmmt) REVERT: J 108 ASP cc_start: 0.6558 (m-30) cc_final: 0.6020 (m-30) REVERT: J 172 LEU cc_start: 0.7915 (tp) cc_final: 0.7712 (tp) REVERT: J 183 PHE cc_start: 0.8720 (p90) cc_final: 0.8264 (p90) REVERT: J 243 TYR cc_start: 0.8049 (m-80) cc_final: 0.7442 (m-80) REVERT: J 254 PHE cc_start: 0.6888 (t80) cc_final: 0.6338 (t80) REVERT: J 278 MET cc_start: 0.5276 (ttp) cc_final: 0.4596 (ttm) REVERT: J 293 TYR cc_start: 0.7451 (p90) cc_final: 0.6927 (p90) REVERT: J 327 PHE cc_start: 0.8335 (m-80) cc_final: 0.8090 (m-80) REVERT: J 632 TYR cc_start: 0.8816 (m-80) cc_final: 0.8515 (m-80) REVERT: J 696 MET cc_start: 0.2798 (ptt) cc_final: 0.2218 (ptt) REVERT: C 80 MET cc_start: 0.6133 (ttm) cc_final: 0.4379 (ttm) REVERT: I 757 MET cc_start: 0.6551 (mtt) cc_final: 0.5583 (mmt) REVERT: I 809 TYR cc_start: 0.7556 (t80) cc_final: 0.7284 (t80) REVERT: I 893 LEU cc_start: 0.8560 (mt) cc_final: 0.8281 (mt) REVERT: I 913 MET cc_start: 0.7812 (mtm) cc_final: 0.7518 (mtm) REVERT: I 921 ARG cc_start: 0.6208 (ttm170) cc_final: 0.4488 (pmt-80) REVERT: I 943 MET cc_start: 0.8023 (tpp) cc_final: 0.7405 (tpt) REVERT: I 1074 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7229 (tpp-160) REVERT: F 108 ASP cc_start: 0.6490 (m-30) cc_final: 0.6046 (m-30) REVERT: F 116 PHE cc_start: 0.7261 (p90) cc_final: 0.7056 (p90) REVERT: F 172 LEU cc_start: 0.7919 (tp) cc_final: 0.7584 (tp) REVERT: F 180 LEU cc_start: 0.9013 (tt) cc_final: 0.8686 (mt) REVERT: F 183 PHE cc_start: 0.8601 (p90) cc_final: 0.8331 (p90) REVERT: F 243 TYR cc_start: 0.7947 (m-80) cc_final: 0.7535 (m-80) REVERT: F 254 PHE cc_start: 0.6433 (t80) cc_final: 0.6029 (t80) REVERT: F 266 PHE cc_start: 0.8749 (m-80) cc_final: 0.8219 (m-80) REVERT: F 278 MET cc_start: 0.5893 (mmm) cc_final: 0.2958 (mpp) REVERT: F 327 PHE cc_start: 0.8310 (m-80) cc_final: 0.7994 (m-80) REVERT: F 674 PHE cc_start: 0.8706 (m-80) cc_final: 0.8474 (m-10) REVERT: F 686 MET cc_start: 0.5233 (mmp) cc_final: 0.4723 (mmm) REVERT: F 689 TYR cc_start: 0.8183 (p90) cc_final: 0.7970 (p90) REVERT: F 696 MET cc_start: 0.2661 (ptt) cc_final: 0.2322 (ptt) REVERT: D 18 VAL cc_start: 0.9586 (p) cc_final: 0.9198 (p) REVERT: D 80 MET cc_start: 0.6296 (ttm) cc_final: 0.5195 (ttm) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.1800 time to fit residues: 93.9983 Evaluate side-chains 252 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 333 optimal weight: 6.9990 chunk 239 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 307 optimal weight: 20.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 60 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E1104 ASN E1132 ASN E1163 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.078328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.060722 restraints weight = 220734.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.061326 restraints weight = 191667.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.061870 restraints weight = 159869.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.062188 restraints weight = 137721.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.062190 restraints weight = 126522.558| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29433 Z= 0.162 Angle : 0.712 9.707 40143 Z= 0.364 Chirality : 0.048 0.525 4647 Planarity : 0.005 0.045 5061 Dihedral : 7.033 58.124 5487 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.07 % Favored : 93.68 % Rotamer: Outliers : 0.07 % Allowed : 0.92 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3543 helix: -0.32 (0.19), residues: 666 sheet: -0.81 (0.18), residues: 759 loop : -1.08 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 822 TYR 0.044 0.002 TYR A 909 PHE 0.028 0.002 PHE I 850 TRP 0.061 0.003 TRP C 50 HIS 0.004 0.001 HIS E1146 Details of bonding type rmsd covalent geometry : bond 0.00343 (29313) covalent geometry : angle 0.69249 (39825) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.01272 ( 84) hydrogen bonds : bond 0.04736 ( 1154) hydrogen bonds : angle 6.41513 ( 3024) link_ALPHA1-3 : bond 0.01597 ( 3) link_ALPHA1-3 : angle 1.55937 ( 9) link_ALPHA1-6 : bond 0.00605 ( 3) link_ALPHA1-6 : angle 1.52459 ( 9) link_BETA1-4 : bond 0.00474 ( 30) link_BETA1-4 : angle 1.90269 ( 90) link_NAG-ASN : bond 0.00402 ( 42) link_NAG-ASN : angle 2.51785 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5895 (mmt) cc_final: 0.5023 (tpp) REVERT: A 833 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6870 (tp-100) REVERT: A 906 MET cc_start: 0.1365 (ttm) cc_final: 0.0978 (tmm) REVERT: A 913 MET cc_start: 0.8632 (mpp) cc_final: 0.8288 (mpp) REVERT: A 921 ARG cc_start: 0.5661 (ttm170) cc_final: 0.4047 (pmt-80) REVERT: A 943 MET cc_start: 0.7936 (tpp) cc_final: 0.7543 (tpt) REVERT: A 1090 GLU cc_start: 0.8485 (mm-30) cc_final: 0.6959 (pp20) REVERT: B 161 MET cc_start: 0.4386 (mmp) cc_final: 0.4117 (mmm) REVERT: B 172 LEU cc_start: 0.8027 (tp) cc_final: 0.7762 (tp) REVERT: B 183 PHE cc_start: 0.8387 (p90) cc_final: 0.7924 (p90) REVERT: B 228 PHE cc_start: 0.9249 (t80) cc_final: 0.9042 (t80) REVERT: B 243 TYR cc_start: 0.7905 (m-80) cc_final: 0.7341 (m-80) REVERT: B 278 MET cc_start: 0.6367 (tpp) cc_final: 0.6150 (ttm) REVERT: B 293 TYR cc_start: 0.7341 (p90) cc_final: 0.6489 (p90) REVERT: B 327 PHE cc_start: 0.8413 (m-80) cc_final: 0.8145 (m-80) REVERT: B 689 TYR cc_start: 0.8152 (p90) cc_final: 0.7891 (p90) REVERT: B 696 MET cc_start: 0.2401 (ptt) cc_final: 0.2026 (ptt) REVERT: H 80 MET cc_start: 0.6911 (ttm) cc_final: 0.6427 (ttm) REVERT: L 1 GLN cc_start: 0.8118 (pm20) cc_final: 0.7606 (pp30) REVERT: E 757 MET cc_start: 0.6356 (mmt) cc_final: 0.5548 (tpt) REVERT: E 906 MET cc_start: 0.0985 (ttm) cc_final: 0.0550 (tmm) REVERT: E 913 MET cc_start: 0.8661 (mpp) cc_final: 0.8161 (mpp) REVERT: E 921 ARG cc_start: 0.5433 (ttm170) cc_final: 0.3667 (pmt-80) REVERT: E 943 MET cc_start: 0.8183 (tpp) cc_final: 0.7905 (tpp) REVERT: E 1021 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8482 (mmtm) REVERT: E 1090 GLU cc_start: 0.8147 (mm-30) cc_final: 0.6875 (pp20) REVERT: E 1102 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8623 (mmmt) REVERT: J 108 ASP cc_start: 0.6483 (m-30) cc_final: 0.5812 (m-30) REVERT: J 148 MET cc_start: 0.9367 (tpt) cc_final: 0.9028 (tpp) REVERT: J 172 LEU cc_start: 0.7823 (tp) cc_final: 0.7578 (tp) REVERT: J 183 PHE cc_start: 0.8569 (p90) cc_final: 0.8118 (p90) REVERT: J 228 PHE cc_start: 0.9395 (t80) cc_final: 0.9110 (t80) REVERT: J 243 TYR cc_start: 0.7918 (m-80) cc_final: 0.7340 (m-80) REVERT: J 278 MET cc_start: 0.5522 (ttp) cc_final: 0.5055 (ttm) REVERT: J 327 PHE cc_start: 0.8411 (m-80) cc_final: 0.8098 (m-80) REVERT: J 606 TYR cc_start: 0.7708 (p90) cc_final: 0.7392 (p90) REVERT: J 632 TYR cc_start: 0.8758 (m-80) cc_final: 0.8509 (m-80) REVERT: J 696 MET cc_start: 0.2848 (ptt) cc_final: 0.2329 (ptt) REVERT: I 757 MET cc_start: 0.6698 (mtt) cc_final: 0.5603 (mmt) REVERT: I 809 TYR cc_start: 0.7512 (t80) cc_final: 0.7245 (t80) REVERT: I 913 MET cc_start: 0.8072 (mtm) cc_final: 0.7842 (mtm) REVERT: I 921 ARG cc_start: 0.6349 (ttm170) cc_final: 0.4657 (pmt-80) REVERT: I 943 MET cc_start: 0.8132 (tpp) cc_final: 0.7568 (tpt) REVERT: I 1074 ARG cc_start: 0.7453 (mmt90) cc_final: 0.7202 (tpp-160) REVERT: I 1090 GLU cc_start: 0.8214 (mm-30) cc_final: 0.6560 (pp20) REVERT: F 108 ASP cc_start: 0.6444 (m-30) cc_final: 0.5995 (m-30) REVERT: F 172 LEU cc_start: 0.8025 (tp) cc_final: 0.7656 (tp) REVERT: F 180 LEU cc_start: 0.9016 (tt) cc_final: 0.8762 (mt) REVERT: F 183 PHE cc_start: 0.8612 (p90) cc_final: 0.8359 (p90) REVERT: F 226 ASN cc_start: 0.9512 (m-40) cc_final: 0.9293 (p0) REVERT: F 243 TYR cc_start: 0.7955 (m-80) cc_final: 0.7519 (m-80) REVERT: F 278 MET cc_start: 0.5828 (mmm) cc_final: 0.3170 (ttm) REVERT: F 293 TYR cc_start: 0.7670 (p90) cc_final: 0.6950 (p90) REVERT: F 327 PHE cc_start: 0.8385 (m-80) cc_final: 0.8004 (m-80) REVERT: F 632 TYR cc_start: 0.8732 (m-80) cc_final: 0.8079 (m-80) REVERT: F 674 PHE cc_start: 0.8689 (m-80) cc_final: 0.8361 (m-80) REVERT: F 686 MET cc_start: 0.5359 (mmp) cc_final: 0.4830 (mmm) REVERT: F 689 TYR cc_start: 0.8207 (p90) cc_final: 0.7939 (p90) REVERT: F 696 MET cc_start: 0.2633 (ptt) cc_final: 0.2212 (ptt) REVERT: D 82 PHE cc_start: 0.9389 (m-80) cc_final: 0.9132 (m-10) REVERT: K 33 MET cc_start: 0.9286 (tpt) cc_final: 0.8992 (tpt) outliers start: 2 outliers final: 0 residues processed: 333 average time/residue: 0.1772 time to fit residues: 95.6509 Evaluate side-chains 255 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 66 optimal weight: 10.0000 chunk 91 optimal weight: 0.0370 chunk 253 optimal weight: 8.9990 chunk 232 optimal weight: 30.0000 chunk 333 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 overall best weight: 3.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 81 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** K 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 = 0.4048 r_free = 0.4048 target = 0.077971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.060028 restraints weight = 221223.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.060832 restraints weight = 192551.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.061504 restraints weight = 163381.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.061781 restraints weight = 145788.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.062133 restraints weight = 135483.494| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29433 Z= 0.171 Angle : 0.710 9.695 40143 Z= 0.365 Chirality : 0.047 0.523 4647 Planarity : 0.005 0.045 5061 Dihedral : 7.031 58.059 5487 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.14 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3543 helix: -0.11 (0.19), residues: 630 sheet: -0.81 (0.17), residues: 840 loop : -1.06 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1069 TYR 0.040 0.002 TYR A 909 PHE 0.025 0.002 PHE I 850 TRP 0.065 0.003 TRP D 50 HIS 0.011 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00363 (29313) covalent geometry : angle 0.69097 (39825) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.07719 ( 84) hydrogen bonds : bond 0.04733 ( 1154) hydrogen bonds : angle 6.44208 ( 3024) link_ALPHA1-3 : bond 0.01342 ( 3) link_ALPHA1-3 : angle 1.49441 ( 9) link_ALPHA1-6 : bond 0.00380 ( 3) link_ALPHA1-6 : angle 1.69681 ( 9) link_BETA1-4 : bond 0.00417 ( 30) link_BETA1-4 : angle 1.93591 ( 90) link_NAG-ASN : bond 0.00412 ( 42) link_NAG-ASN : angle 2.43769 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.079 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: 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 757 MET cc_start: 0.5880 (mmt) cc_final: 0.5059 (tpp) REVERT: A 833 GLN cc_start: 0.7046 (tp-100) cc_final: 0.6798 (tp40) REVERT: A 906 MET cc_start: 0.1321 (ttm) cc_final: 0.0940 (tmm) REVERT: A 913 MET cc_start: 0.8757 (mpp) cc_final: 0.8329 (mpp) REVERT: A 921 ARG cc_start: 0.5751 (ttm170) cc_final: 0.4213 (pmt-80) REVERT: A 939 MET cc_start: 0.4785 (mpp) cc_final: 0.3759 (mmm) REVERT: A 943 MET cc_start: 0.7909 (tpp) cc_final: 0.7494 (tpt) REVERT: A 1090 GLU cc_start: 0.8441 (mm-30) cc_final: 0.6910 (pp20) REVERT: B 108 ASP cc_start: 0.6199 (m-30) cc_final: 0.5974 (m-30) REVERT: B 116 PHE cc_start: 0.6923 (p90) cc_final: 0.6627 (p90) REVERT: B 172 LEU cc_start: 0.8010 (tp) cc_final: 0.7763 (tp) REVERT: B 183 PHE cc_start: 0.8353 (p90) cc_final: 0.7929 (p90) REVERT: B 228 PHE cc_start: 0.9290 (t80) cc_final: 0.9083 (t80) REVERT: B 243 TYR cc_start: 0.7988 (m-80) cc_final: 0.7430 (m-80) REVERT: B 266 PHE cc_start: 0.8661 (m-80) cc_final: 0.8286 (m-80) REVERT: B 278 MET cc_start: 0.6222 (tpp) cc_final: 0.5645 (ttm) REVERT: B 293 TYR cc_start: 0.7406 (p90) cc_final: 0.6748 (p90) REVERT: B 315 VAL cc_start: 0.8322 (p) cc_final: 0.8024 (p) REVERT: B 327 PHE cc_start: 0.8348 (m-80) cc_final: 0.8141 (m-80) REVERT: B 689 TYR cc_start: 0.8082 (p90) cc_final: 0.7844 (p90) REVERT: B 696 MET cc_start: 0.2316 (ptt) cc_final: 0.1976 (ptt) REVERT: H 80 MET cc_start: 0.6773 (ttm) cc_final: 0.6328 (ttm) REVERT: H 100 MET cc_start: -0.1813 (mmt) cc_final: -0.2077 (mmt) REVERT: L 35 TRP cc_start: 0.7594 (m-90) cc_final: 0.7343 (m-90) REVERT: E 757 MET cc_start: 0.6312 (mmt) cc_final: 0.5532 (tpt) REVERT: E 906 MET cc_start: 0.0904 (ttm) cc_final: 0.0466 (tmm) REVERT: E 913 MET cc_start: 0.8704 (mpp) cc_final: 0.8155 (mpp) REVERT: E 921 ARG cc_start: 0.5524 (ttm170) cc_final: 0.3791 (pmt-80) REVERT: E 943 MET cc_start: 0.8151 (tpp) cc_final: 0.7637 (tpt) REVERT: E 1021 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8465 (mmtm) REVERT: E 1090 GLU cc_start: 0.8107 (mm-30) cc_final: 0.6860 (pp20) REVERT: E 1102 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8579 (mmmt) REVERT: J 108 ASP cc_start: 0.6431 (m-30) cc_final: 0.5764 (m-30) REVERT: J 148 MET cc_start: 0.9394 (tpt) cc_final: 0.9094 (tpp) REVERT: J 172 LEU cc_start: 0.7768 (tp) cc_final: 0.7524 (tp) REVERT: J 183 PHE cc_start: 0.8578 (p90) cc_final: 0.8105 (p90) REVERT: J 228 PHE cc_start: 0.9391 (t80) cc_final: 0.9104 (t80) REVERT: J 243 TYR cc_start: 0.7912 (m-80) cc_final: 0.7315 (m-80) REVERT: J 278 MET cc_start: 0.5532 (ttp) cc_final: 0.5099 (ttm) REVERT: J 293 TYR cc_start: 0.7446 (p90) cc_final: 0.7139 (p90) REVERT: J 327 PHE cc_start: 0.8399 (m-80) cc_final: 0.8139 (m-80) REVERT: J 606 TYR cc_start: 0.7699 (p90) cc_final: 0.7391 (p90) REVERT: J 696 MET cc_start: 0.2738 (ptt) cc_final: 0.2209 (ptt) REVERT: I 757 MET cc_start: 0.6496 (mtt) cc_final: 0.5530 (mmt) REVERT: I 809 TYR cc_start: 0.7639 (t80) cc_final: 0.7403 (t80) REVERT: I 913 MET cc_start: 0.8104 (mtm) cc_final: 0.7865 (mtm) REVERT: I 921 ARG cc_start: 0.6346 (ttm170) cc_final: 0.4720 (pmt-80) REVERT: I 943 MET cc_start: 0.7933 (tpp) cc_final: 0.7280 (tpt) REVERT: I 1074 ARG cc_start: 0.7419 (mmt90) cc_final: 0.7148 (tpp-160) REVERT: I 1090 GLU cc_start: 0.8297 (mm-30) cc_final: 0.6613 (pp20) REVERT: F 172 LEU cc_start: 0.7915 (tp) cc_final: 0.7528 (tp) REVERT: F 180 LEU cc_start: 0.9042 (tt) cc_final: 0.8776 (mt) REVERT: F 183 PHE cc_start: 0.8652 (p90) cc_final: 0.8375 (p90) REVERT: F 226 ASN cc_start: 0.9511 (m-40) cc_final: 0.9266 (p0) REVERT: F 243 TYR cc_start: 0.8010 (m-80) cc_final: 0.7570 (m-80) REVERT: F 266 PHE cc_start: 0.8696 (m-80) cc_final: 0.8183 (m-80) REVERT: F 278 MET cc_start: 0.5864 (mmm) cc_final: 0.3415 (ttt) REVERT: F 293 TYR cc_start: 0.7722 (p90) cc_final: 0.7207 (p90) REVERT: F 315 VAL cc_start: 0.8382 (p) cc_final: 0.8122 (p) REVERT: F 327 PHE cc_start: 0.8306 (m-80) cc_final: 0.7927 (m-80) REVERT: F 674 PHE cc_start: 0.8594 (m-80) cc_final: 0.8262 (m-80) REVERT: F 689 TYR cc_start: 0.8189 (p90) cc_final: 0.7926 (p90) REVERT: F 696 MET cc_start: 0.2569 (ptt) cc_final: 0.2118 (ptt) REVERT: D 68 GLN cc_start: 0.0784 (OUTLIER) cc_final: 0.0579 (tm-30) REVERT: D 82 PHE cc_start: 0.9308 (m-80) cc_final: 0.8882 (m-10) REVERT: D 100 MET cc_start: -0.1532 (mmt) cc_final: -0.2223 (mmt) REVERT: K 33 MET cc_start: 0.9203 (tpt) cc_final: 0.8827 (tpt) REVERT: K 50 THR cc_start: 0.6754 (m) cc_final: 0.6444 (m) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.1823 time to fit residues: 95.8578 Evaluate side-chains 259 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 75 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 chunk 90 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.078032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.060197 restraints weight = 220002.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.060914 restraints weight = 193055.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.061533 restraints weight = 165061.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.061847 restraints weight = 144757.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.062263 restraints weight = 132243.811| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29433 Z= 0.170 Angle : 0.714 9.692 40143 Z= 0.366 Chirality : 0.047 0.502 4647 Planarity : 0.005 0.080 5061 Dihedral : 7.030 58.139 5487 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.14 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3543 helix: -0.26 (0.19), residues: 645 sheet: -0.80 (0.18), residues: 810 loop : -1.09 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1069 TYR 0.039 0.002 TYR A 909 PHE 0.031 0.002 PHE A1116 TRP 0.053 0.004 TRP D 50 HIS 0.013 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00363 (29313) covalent geometry : angle 0.69524 (39825) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.15622 ( 84) hydrogen bonds : bond 0.04640 ( 1154) hydrogen bonds : angle 6.49341 ( 3024) link_ALPHA1-3 : bond 0.01364 ( 3) link_ALPHA1-3 : angle 1.50421 ( 9) link_ALPHA1-6 : bond 0.00264 ( 3) link_ALPHA1-6 : angle 1.79665 ( 9) link_BETA1-4 : bond 0.00414 ( 30) link_BETA1-4 : angle 1.95694 ( 90) link_NAG-ASN : bond 0.00396 ( 42) link_NAG-ASN : angle 2.41315 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: 0.5925 (mmt) cc_final: 0.5070 (tpt) REVERT: A 833 GLN cc_start: 0.7041 (tp-100) cc_final: 0.6801 (tp40) REVERT: A 906 MET cc_start: 0.1279 (ttm) cc_final: 0.0862 (tmm) REVERT: A 913 MET cc_start: 0.8713 (mpp) cc_final: 0.8274 (mpp) REVERT: A 921 ARG cc_start: 0.5958 (ttm170) cc_final: 0.4464 (pmt-80) REVERT: A 939 MET cc_start: 0.4807 (mpp) cc_final: 0.4026 (mmm) REVERT: A 943 MET cc_start: 0.7834 (tpp) cc_final: 0.7403 (tpp) REVERT: A 1090 GLU cc_start: 0.8471 (mm-30) cc_final: 0.6921 (pp20) REVERT: B 108 ASP cc_start: 0.6380 (m-30) cc_final: 0.6111 (m-30) REVERT: B 156 PHE cc_start: 0.8603 (m-80) cc_final: 0.8381 (m-80) REVERT: B 161 MET cc_start: 0.5922 (mmm) cc_final: 0.5689 (mmp) REVERT: B 172 LEU cc_start: 0.7950 (tp) cc_final: 0.7691 (tp) REVERT: B 183 PHE cc_start: 0.8334 (p90) cc_final: 0.7872 (p90) REVERT: B 243 TYR cc_start: 0.7993 (m-80) cc_final: 0.7471 (m-80) REVERT: B 254 PHE cc_start: 0.6756 (t80) cc_final: 0.6365 (t80) REVERT: B 278 MET cc_start: 0.6275 (tpp) cc_final: 0.5548 (ttt) REVERT: B 293 TYR cc_start: 0.7342 (p90) cc_final: 0.6612 (p90) REVERT: B 327 PHE cc_start: 0.8418 (m-80) cc_final: 0.8154 (m-80) REVERT: B 689 TYR cc_start: 0.8125 (p90) cc_final: 0.7847 (p90) REVERT: B 696 MET cc_start: 0.2146 (ptt) cc_final: 0.1621 (ptt) REVERT: H 100 MET cc_start: -0.2050 (mmt) cc_final: -0.2322 (mmp) REVERT: L 35 TRP cc_start: 0.7604 (m-90) cc_final: 0.7390 (m-90) REVERT: E 757 MET cc_start: 0.6133 (mmt) cc_final: 0.5283 (tpt) REVERT: E 906 MET cc_start: 0.1145 (ttm) cc_final: 0.0887 (tmm) REVERT: E 913 MET cc_start: 0.8710 (mpp) cc_final: 0.8172 (mpp) REVERT: E 921 ARG cc_start: 0.5697 (ttm170) cc_final: 0.3979 (pmt-80) REVERT: E 943 MET cc_start: 0.8204 (tpp) cc_final: 0.7596 (tpt) REVERT: E 1021 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8494 (mmtm) REVERT: E 1090 GLU cc_start: 0.8089 (mm-30) cc_final: 0.6893 (pp20) REVERT: E 1102 LYS cc_start: 0.8828 (mmpt) cc_final: 0.8481 (mmmt) REVERT: J 108 ASP cc_start: 0.6403 (m-30) cc_final: 0.5774 (m-30) REVERT: J 148 MET cc_start: 0.9393 (tpt) cc_final: 0.9097 (tpp) REVERT: J 172 LEU cc_start: 0.7785 (tp) cc_final: 0.7531 (tp) REVERT: J 183 PHE cc_start: 0.8504 (p90) cc_final: 0.8028 (p90) REVERT: J 228 PHE cc_start: 0.9382 (t80) cc_final: 0.9087 (t80) REVERT: J 243 TYR cc_start: 0.7946 (m-80) cc_final: 0.7338 (m-80) REVERT: J 266 PHE cc_start: 0.8846 (m-10) cc_final: 0.8547 (m-80) REVERT: J 278 MET cc_start: 0.5970 (ttp) cc_final: 0.5507 (ttm) REVERT: J 293 TYR cc_start: 0.7405 (p90) cc_final: 0.7035 (p90) REVERT: J 327 PHE cc_start: 0.8425 (m-80) cc_final: 0.8161 (m-80) REVERT: J 606 TYR cc_start: 0.7680 (p90) cc_final: 0.7364 (p90) REVERT: J 632 TYR cc_start: 0.8968 (m-80) cc_final: 0.8746 (m-80) REVERT: J 696 MET cc_start: 0.2563 (ptt) cc_final: 0.2068 (ptt) REVERT: I 757 MET cc_start: 0.6404 (mtt) cc_final: 0.5460 (mmt) REVERT: I 809 TYR cc_start: 0.7662 (t80) cc_final: 0.7427 (t80) REVERT: I 921 ARG cc_start: 0.6425 (ttm170) cc_final: 0.4848 (pmt-80) REVERT: I 943 MET cc_start: 0.8072 (tpp) cc_final: 0.7367 (tpt) REVERT: I 1090 GLU cc_start: 0.8325 (mm-30) cc_final: 0.6600 (pp20) REVERT: F 108 ASP cc_start: 0.6150 (m-30) cc_final: 0.5913 (m-30) REVERT: F 172 LEU cc_start: 0.7848 (tp) cc_final: 0.7477 (tp) REVERT: F 180 LEU cc_start: 0.9012 (tt) cc_final: 0.8766 (mt) REVERT: F 183 PHE cc_start: 0.8617 (p90) cc_final: 0.8348 (p90) REVERT: F 226 ASN cc_start: 0.9503 (m-40) cc_final: 0.9255 (p0) REVERT: F 243 TYR cc_start: 0.8000 (m-80) cc_final: 0.7549 (m-80) REVERT: F 266 PHE cc_start: 0.8715 (m-80) cc_final: 0.8201 (m-80) REVERT: F 277 ASN cc_start: 0.6982 (m-40) cc_final: 0.6191 (m-40) REVERT: F 278 MET cc_start: 0.5592 (mmm) cc_final: 0.3367 (ttt) REVERT: F 293 TYR cc_start: 0.7714 (p90) cc_final: 0.7148 (p90) REVERT: F 315 VAL cc_start: 0.8363 (p) cc_final: 0.8121 (p) REVERT: F 327 PHE cc_start: 0.8287 (m-80) cc_final: 0.7913 (m-80) REVERT: F 674 PHE cc_start: 0.8598 (m-80) cc_final: 0.8254 (m-80) REVERT: F 689 TYR cc_start: 0.8254 (p90) cc_final: 0.7990 (p90) REVERT: F 696 MET cc_start: 0.2273 (ptt) cc_final: 0.1899 (ptt) REVERT: D 80 MET cc_start: 0.6317 (ttm) cc_final: 0.5356 (ttm) REVERT: D 100 MET cc_start: -0.1004 (mmt) cc_final: -0.1535 (mmt) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.1783 time to fit residues: 94.4251 Evaluate side-chains 260 residues out of total 3033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 315 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 81 GLN G 6 GLN I1138 HIS F 348 HIS ** F 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.080145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.062048 restraints weight = 218789.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.062764 restraints weight = 191831.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.063067 restraints weight = 164044.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.063711 restraints weight = 149470.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.063711 restraints weight = 133663.648| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29433 Z= 0.127 Angle : 0.665 9.741 40143 Z= 0.340 Chirality : 0.046 0.366 4647 Planarity : 0.005 0.047 5061 Dihedral : 6.566 57.371 5487 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.12 % Favored : 93.62 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3543 helix: 0.15 (0.19), residues: 648 sheet: -0.72 (0.17), residues: 837 loop : -0.99 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1069 TYR 0.036 0.002 TYR A 909 PHE 0.037 0.002 PHE E1019 TRP 0.051 0.003 TRP D 50 HIS 0.008 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00275 (29313) covalent geometry : angle 0.64766 (39825) SS BOND : bond 0.00354 ( 42) SS BOND : angle 1.30330 ( 84) hydrogen bonds : bond 0.04210 ( 1154) hydrogen bonds : angle 6.12179 ( 3024) link_ALPHA1-3 : bond 0.01302 ( 3) link_ALPHA1-3 : angle 1.47092 ( 9) link_ALPHA1-6 : bond 0.00507 ( 3) link_ALPHA1-6 : angle 1.65567 ( 9) link_BETA1-4 : bond 0.00441 ( 30) link_BETA1-4 : angle 1.82379 ( 90) link_NAG-ASN : bond 0.00264 ( 42) link_NAG-ASN : angle 2.14392 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.90 seconds wall clock time: 92 minutes 55.41 seconds (5575.41 seconds total)