Starting phenix.real_space_refine on Wed Nov 19 01:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.map" model { file = "/net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mar_9062/11_2025/6mar_9062.cif" } resolution = 4.5 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= 0.005 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 116 5.16 5 C 12000 2.51 5 N 3158 2.21 5 O 3937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19211 Number of models: 1 Model: "" Number of chains: 47 Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1050 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain breaks: 1 Chain: "C" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3448 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "G" 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: 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: "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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "T" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "U" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "i" 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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: "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: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" 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: "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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.27 Number of scatterers: 19211 At special positions: 0 Unit cell: (158.4, 142.8, 128.4, 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 116 16.00 O 3937 8.00 N 3158 7.00 C 12000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 9 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " MAN h 6 " - " MAN h 7 " " BMA n 3 " - " MAN n 9 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " BMA h 3 " - " MAN h 6 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 8 " BETA1-2 " MAN T 4 " - " NAG T 5 " " MAN T 9 " - " NAG T 10 " " MAN U 4 " - " NAG U 5 " " MAN U 8 " - " NAG U 9 " " MAN n 4 " - " NAG n 5 " " MAN o 4 " - " NAG o 5 " " MAN o 8 " - " NAG o 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG T 5 " - " GAL T 6 " " NAG T 7 " - " GAL T 8 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " MAN U 4 " - " NAG U 7 " " NAG U 5 " - " GAL U 6 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG n 5 " - " GAL n 6 " " NAG n 7 " - " GAL n 8 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " MAN o 4 " - " NAG o 7 " " NAG o 5 " - " GAL o 6 " BETA1-6 " NAG T 1 " - " FUC T 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN T 4 " - " NAG T 7 " " NAG U 1 " - " FUC U 10 " " NAG n 1 " - " FUC n 10 " " MAN n 4 " - " NAG n 7 " " NAG o 1 " - " FUC o 10 " NAG-ASN " NAG A1000 " - " ASN A 295 " " NAG A1015 " - " ASN A 355 " " NAG A1018 " - " ASN A 392 " " NAG A1022 " - " ASN A 234 " " NAG A1023 " - " ASN A 276 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG C 601 " - " ASN C 295 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 88 " " NAG C 612 " - " ASN C 392 " " NAG C 615 " - " ASN C 234 " " NAG D1000 " - " ASN D 625 " " NAG D1001 " - " ASN D 618 " " NAG D1004 " - " ASN D 637 " " NAG E1000 " - " ASN E 295 " " NAG E1001 " - " ASN E 301 " " NAG E1015 " - " ASN E 355 " " NAG E1016 " - " ASN E 88 " " NAG E1017 " - " ASN E 392 " " NAG E1021 " - " ASN E 234 " " NAG F1000 " - " ASN F 618 " " NAG G 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN B 611 " " NAG U 1 " - " ASN B 637 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 276 " " NAG c 1 " - " ASN C 160 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN E 448 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 363 " " NAG n 1 " - " ASN F 611 " " NAG o 1 " - " ASN F 637 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 754.6 milliseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4124 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 40 sheets defined 20.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.571A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.793A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.548A pdb=" N THR H 87 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.802A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.885A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.964A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.356A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 483 " --> pdb=" O TRP A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.631A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.124A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.810A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.667A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.638A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.263A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 565 Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.013A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.845A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 650 Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'C' and resid 67 through 71 removed outlier: 4.500A pdb=" N THR C 71 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.623A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.740A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.610A pdb=" N ASN C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 381 removed outlier: 4.039A pdb=" N GLY C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.983A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.847A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.961A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.039A pdb=" N ARG E 143 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.892A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 4.015A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 4.019A pdb=" N GLY E 380 " --> pdb=" O ASN E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.550A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN E 392 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.714A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.893A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.724A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.639A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'F' and resid 655 through 663 removed outlier: 3.592A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.681A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL M 37 " --> pdb=" O ARG M 91 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 20 through 23 Processing sheet with id=AA3, first strand: chain 'M' and resid 94 through 95 removed outlier: 7.293A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 100K through 100L Processing sheet with id=AA5, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.508A pdb=" N THR N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG N 74 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.250A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.606A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.719A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA H 93 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.267A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.633A pdb=" N MET H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 100M through 100N Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 7.041A pdb=" N ASN L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 35 through 45 removed outlier: 4.042A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.180A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.792A pdb=" N MET A 161 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.149A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.380A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.549A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.702A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AC5, first strand: chain 'D' and resid 604 through 609 removed outlier: 3.988A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.609A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.843A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.778A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 170 through 176 removed outlier: 3.522A pdb=" N MET C 161 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 191 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.089A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 424 " --> pdb=" O MET C 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.694A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.694A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 383 through 385 removed outlier: 3.813A pdb=" N ILE C 414 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.590A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AD7, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.696A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AD9, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.036A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.780A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.629A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 469 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 374 through 376 removed outlier: 3.962A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 307 through 312 removed outlier: 6.782A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1329 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: 3.64 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5901 1.34 - 1.46: 4949 1.46 - 1.59: 8558 1.59 - 1.71: 2 1.71 - 1.83: 164 Bond restraints: 19574 Sorted by residual: bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.91e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C1 BMA o 3 " pdb=" C2 BMA o 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 19569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 25027 2.01 - 4.02: 1291 4.02 - 6.03: 174 6.03 - 8.04: 55 8.04 - 10.05: 17 Bond angle restraints: 26564 Sorted by residual: angle pdb=" C MET C 426 " pdb=" N TRP C 427 " pdb=" CA TRP C 427 " ideal model delta sigma weight residual 121.19 128.68 -7.49 1.59e+00 3.96e-01 2.22e+01 angle pdb=" C ALA C 70 " pdb=" N THR C 71 " pdb=" CA THR C 71 " ideal model delta sigma weight residual 122.46 128.87 -6.41 1.41e+00 5.03e-01 2.07e+01 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 110.24 115.31 -5.07 1.30e+00 5.92e-01 1.52e+01 angle pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta sigma weight residual 120.82 126.54 -5.72 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C ALA A 70 " pdb=" N THR A 71 " pdb=" CA THR A 71 " ideal model delta sigma weight residual 122.41 130.50 -8.09 2.09e+00 2.29e-01 1.50e+01 ... (remaining 26559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 12721 24.09 - 48.18: 429 48.18 - 72.26: 111 72.26 - 96.35: 69 96.35 - 120.44: 72 Dihedral angle restraints: 13402 sinusoidal: 7006 harmonic: 6396 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -155.18 69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -153.59 67.59 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -152.29 66.29 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3167 0.115 - 0.230: 173 0.230 - 0.345: 16 0.345 - 0.461: 9 0.461 - 0.576: 3 Chirality restraints: 3368 Sorted by residual: chirality pdb=" C1 NAG E1015 " pdb=" ND2 ASN E 355 " pdb=" C2 NAG E1015 " pdb=" O5 NAG E1015 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 3365 not shown) Planarity restraints: 3253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 497 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO C 498 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 32 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO M 33 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO M 33 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 33 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 469 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.47e+00 pdb=" N PRO E 470 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 470 " -0.040 5.00e-02 4.00e+02 ... (remaining 3250 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 269 2.60 - 3.18: 15749 3.18 - 3.75: 27484 3.75 - 4.33: 37090 4.33 - 4.90: 58411 Nonbonded interactions: 139003 Sorted by model distance: nonbonded pdb=" OE1 GLU N 50 " pdb=" ND2 ASN N 53 " model vdw 2.031 3.120 nonbonded pdb=" O ILE A 424 " pdb=" O ASN A 425 " model vdw 2.035 3.040 nonbonded pdb=" CE2 TRP H 55 " pdb=" O7 NAG T 5 " model vdw 2.078 3.260 nonbonded pdb=" CZ3 TRP H 55 " pdb=" C6 BMA T 3 " model vdw 2.207 3.740 nonbonded pdb=" CD1 TRP H 55 " pdb=" OH TYR H 100M" model vdw 2.221 3.260 ... (remaining 138998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 56 or resid 67 through 396 or resid 412 through \ 1023)) selection = (chain 'C' and (resid 32 through 56 or resid 67 through 396 or resid 412 through \ 615)) selection = (chain 'E' and resid 32 through 1017) } ncs_group { reference = (chain 'B' and resid 521 through 801) selection = (chain 'D' and (resid 521 through 549 or resid 569 through 1000)) selection = (chain 'F' and (resid 521 through 549 or resid 569 through 1000)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'K' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'j' } ncs_group { reference = (chain 'T' and (resid 2 or resid 11)) selection = (chain 'U' and (resid 1 or resid 10)) selection = (chain 'n' and (resid 1 or resid 10)) selection = (chain 'o' and (resid 1 or resid 10)) } 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.230 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.007 0.095 19738 Z= 0.355 Angle : 1.141 15.319 27022 Z= 0.533 Chirality : 0.065 0.576 3368 Planarity : 0.007 0.077 3200 Dihedral : 16.835 120.439 9176 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.81 % Favored : 89.96 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.15), residues: 2181 helix: -1.70 (0.21), residues: 387 sheet: -1.66 (0.20), residues: 564 loop : -2.84 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 298 TYR 0.023 0.003 TYR D 638 PHE 0.031 0.003 PHE A 53 TRP 0.048 0.003 TRP F 614 HIS 0.008 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00742 (19574) covalent geometry : angle 1.03990 (26564) SS BOND : bond 0.00444 ( 34) SS BOND : angle 1.23033 ( 68) hydrogen bonds : bond 0.23938 ( 506) hydrogen bonds : angle 8.48111 ( 1329) link_ALPHA1-2 : bond 0.00260 ( 2) link_ALPHA1-2 : angle 2.21363 ( 6) link_ALPHA1-3 : bond 0.00471 ( 8) link_ALPHA1-3 : angle 2.28952 ( 24) link_ALPHA1-6 : bond 0.00519 ( 6) link_ALPHA1-6 : angle 2.36274 ( 18) link_BETA1-2 : bond 0.00992 ( 7) link_BETA1-2 : angle 2.72807 ( 21) link_BETA1-4 : bond 0.00936 ( 48) link_BETA1-4 : angle 3.89151 ( 144) link_BETA1-6 : bond 0.00329 ( 6) link_BETA1-6 : angle 1.91254 ( 18) link_NAG-ASN : bond 0.00753 ( 53) link_NAG-ASN : angle 4.81789 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 279 time to evaluate : 0.755 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: M 35 TYR cc_start: 0.8259 (m-10) cc_final: 0.7960 (m-10) REVERT: N 93 ASP cc_start: 0.8573 (t0) cc_final: 0.8342 (t0) REVERT: H 31 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8894 (ttmm) REVERT: H 34 MET cc_start: 0.7903 (ptp) cc_final: 0.6367 (mtm) REVERT: H 100 ASP cc_start: 0.8434 (t0) cc_final: 0.8217 (t0) REVERT: A 207 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9114 (tmtt) REVERT: A 211 GLU cc_start: 0.8941 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 368 ASP cc_start: 0.8222 (t0) cc_final: 0.7540 (p0) REVERT: B 530 MET cc_start: 0.7149 (mtp) cc_final: 0.6192 (mtt) REVERT: B 543 ASN cc_start: 0.9320 (m-40) cc_final: 0.8972 (m110) REVERT: B 577 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7839 (tm-30) REVERT: B 584 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8742 (tm-30) REVERT: D 530 MET cc_start: 0.6645 (mtm) cc_final: 0.6290 (ptp) REVERT: D 586 TYR cc_start: 0.9352 (t80) cc_final: 0.8920 (t80) REVERT: D 589 ASP cc_start: 0.8582 (m-30) cc_final: 0.8292 (p0) REVERT: C 45 TRP cc_start: 0.8839 (m-10) cc_final: 0.8612 (m-10) REVERT: C 207 LYS cc_start: 0.9339 (mmtt) cc_final: 0.8700 (tmtt) REVERT: C 424 ILE cc_start: 0.8309 (mm) cc_final: 0.8047 (mm) REVERT: E 104 MET cc_start: 0.9417 (ttm) cc_final: 0.8868 (ttt) REVERT: E 377 ASN cc_start: 0.8403 (t0) cc_final: 0.8113 (p0) REVERT: E 477 ASP cc_start: 0.9420 (m-30) cc_final: 0.8962 (p0) REVERT: F 530 MET cc_start: 0.8235 (mtm) cc_final: 0.7774 (mtm) REVERT: F 575 GLN cc_start: 0.9284 (tt0) cc_final: 0.8956 (tm-30) outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.1740 time to fit residues: 70.9289 Evaluate side-chains 139 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN A 293 GLN A 348 GLN A 352 HIS A 374 HIS A 440 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C 478 ASN E 478 ASN F 540 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041228 restraints weight = 144351.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042404 restraints weight = 87288.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.043262 restraints weight = 61350.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.043864 restraints weight = 47421.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044258 restraints weight = 39217.597| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19738 Z= 0.151 Angle : 0.829 13.226 27022 Z= 0.379 Chirality : 0.049 0.438 3368 Planarity : 0.005 0.065 3200 Dihedral : 16.506 106.376 5039 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.17), residues: 2181 helix: -0.40 (0.25), residues: 387 sheet: -1.46 (0.21), residues: 570 loop : -2.40 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 100J TYR 0.019 0.001 TYR D 643 PHE 0.018 0.002 PHE A 53 TRP 0.019 0.002 TRP B 614 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00319 (19574) covalent geometry : angle 0.74279 (26564) SS BOND : bond 0.00328 ( 34) SS BOND : angle 1.07619 ( 68) hydrogen bonds : bond 0.04872 ( 506) hydrogen bonds : angle 6.60676 ( 1329) link_ALPHA1-2 : bond 0.00732 ( 2) link_ALPHA1-2 : angle 2.19604 ( 6) link_ALPHA1-3 : bond 0.01257 ( 8) link_ALPHA1-3 : angle 2.15532 ( 24) link_ALPHA1-6 : bond 0.00917 ( 6) link_ALPHA1-6 : angle 2.93912 ( 18) link_BETA1-2 : bond 0.00679 ( 7) link_BETA1-2 : angle 2.43219 ( 21) link_BETA1-4 : bond 0.00767 ( 48) link_BETA1-4 : angle 2.68297 ( 144) link_BETA1-6 : bond 0.00660 ( 6) link_BETA1-6 : angle 1.54684 ( 18) link_NAG-ASN : bond 0.00600 ( 53) link_NAG-ASN : angle 3.83560 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.668 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: M 35 TYR cc_start: 0.8526 (m-10) cc_final: 0.8186 (m-10) REVERT: M 95 MET cc_start: 0.8703 (ttt) cc_final: 0.8476 (ttt) REVERT: M 100 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7897 (mtp-110) REVERT: N 93 ASP cc_start: 0.8792 (t0) cc_final: 0.8438 (t0) REVERT: H 100 ASP cc_start: 0.8264 (t0) cc_final: 0.7973 (t0) REVERT: L 33 LEU cc_start: 0.8878 (tp) cc_final: 0.8624 (tp) REVERT: A 95 MET cc_start: 0.8616 (tpp) cc_final: 0.8392 (tpp) REVERT: A 142 MET cc_start: 0.7837 (mmm) cc_final: 0.6556 (mpp) REVERT: A 207 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9190 (tmtt) REVERT: A 211 GLU cc_start: 0.9119 (tt0) cc_final: 0.8796 (tm-30) REVERT: A 302 ASN cc_start: 0.8394 (t0) cc_final: 0.8167 (t0) REVERT: A 368 ASP cc_start: 0.8579 (t0) cc_final: 0.8241 (t0) REVERT: B 530 MET cc_start: 0.7660 (mtp) cc_final: 0.6488 (mtm) REVERT: B 535 MET cc_start: 0.7769 (mpp) cc_final: 0.7494 (mpp) REVERT: B 543 ASN cc_start: 0.9295 (m-40) cc_final: 0.8949 (m110) REVERT: B 647 GLU cc_start: 0.8856 (mp0) cc_final: 0.8615 (mp0) REVERT: D 564 HIS cc_start: 0.7473 (t-90) cc_final: 0.7256 (t-170) REVERT: C 45 TRP cc_start: 0.8855 (m-10) cc_final: 0.8332 (m-90) REVERT: C 207 LYS cc_start: 0.9377 (mmtt) cc_final: 0.8739 (tmtt) REVERT: E 104 MET cc_start: 0.9273 (ttm) cc_final: 0.8916 (ttm) REVERT: E 161 MET cc_start: 0.8643 (tpt) cc_final: 0.8437 (tmm) REVERT: E 420 ILE cc_start: 0.8709 (mt) cc_final: 0.8456 (tt) REVERT: E 434 MET cc_start: 0.9232 (tmm) cc_final: 0.8952 (tmm) REVERT: E 477 ASP cc_start: 0.9525 (m-30) cc_final: 0.9049 (p0) REVERT: F 575 GLN cc_start: 0.9421 (tt0) cc_final: 0.8967 (tm-30) REVERT: F 647 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8582 (mt-10) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1615 time to fit residues: 50.1369 Evaluate side-chains 138 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 8 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 45 optimal weight: 0.0670 chunk 95 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 170 GLN A 478 ASN B 591 GLN B 640 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN C 293 GLN C 330 HIS C 422 GLN F 652 GLN F 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.039405 restraints weight = 149352.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.040564 restraints weight = 89819.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041406 restraints weight = 62850.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041982 restraints weight = 48552.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042417 restraints weight = 40310.770| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19738 Z= 0.243 Angle : 0.898 14.893 27022 Z= 0.406 Chirality : 0.050 0.436 3368 Planarity : 0.005 0.066 3200 Dihedral : 14.832 102.347 5039 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.55 % Favored : 89.41 % Rotamer: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.45 (0.17), residues: 2181 helix: 0.08 (0.26), residues: 386 sheet: -1.48 (0.21), residues: 591 loop : -2.34 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 77 TYR 0.016 0.002 TYR F 586 PHE 0.023 0.002 PHE A 53 TRP 0.019 0.002 TRP F 614 HIS 0.005 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00526 (19574) covalent geometry : angle 0.82384 (26564) SS BOND : bond 0.00542 ( 34) SS BOND : angle 0.96555 ( 68) hydrogen bonds : bond 0.04749 ( 506) hydrogen bonds : angle 6.35846 ( 1329) link_ALPHA1-2 : bond 0.00506 ( 2) link_ALPHA1-2 : angle 2.25187 ( 6) link_ALPHA1-3 : bond 0.01276 ( 8) link_ALPHA1-3 : angle 2.02859 ( 24) link_ALPHA1-6 : bond 0.00680 ( 6) link_ALPHA1-6 : angle 2.43575 ( 18) link_BETA1-2 : bond 0.00672 ( 7) link_BETA1-2 : angle 2.20407 ( 21) link_BETA1-4 : bond 0.00747 ( 48) link_BETA1-4 : angle 2.75402 ( 144) link_BETA1-6 : bond 0.00418 ( 6) link_BETA1-6 : angle 1.65594 ( 18) link_NAG-ASN : bond 0.00553 ( 53) link_NAG-ASN : angle 3.71744 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.763 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: M 35 TYR cc_start: 0.8508 (m-10) cc_final: 0.7516 (m-10) REVERT: M 95 MET cc_start: 0.8974 (ttt) cc_final: 0.7971 (ttt) REVERT: N 93 ASP cc_start: 0.8814 (t0) cc_final: 0.8510 (t0) REVERT: H 100 ASP cc_start: 0.8364 (t0) cc_final: 0.8106 (t0) REVERT: A 207 LYS cc_start: 0.9484 (mmtt) cc_final: 0.9187 (tmtt) REVERT: A 302 ASN cc_start: 0.8460 (t0) cc_final: 0.8144 (t0) REVERT: A 368 ASP cc_start: 0.8599 (t0) cc_final: 0.8329 (t70) REVERT: B 530 MET cc_start: 0.7728 (mtp) cc_final: 0.6625 (mtm) REVERT: B 535 MET cc_start: 0.8063 (mpp) cc_final: 0.7765 (mpp) REVERT: C 104 MET cc_start: 0.9446 (ttm) cc_final: 0.9184 (ttm) REVERT: C 207 LYS cc_start: 0.9421 (mmtt) cc_final: 0.8665 (tmtt) REVERT: E 104 MET cc_start: 0.9378 (ttm) cc_final: 0.9036 (ttm) REVERT: E 142 MET cc_start: 0.5511 (mmm) cc_final: 0.4097 (mpp) REVERT: E 477 ASP cc_start: 0.9569 (m-30) cc_final: 0.9056 (p0) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1586 time to fit residues: 38.2639 Evaluate side-chains 119 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 173 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 212 optimal weight: 0.0870 chunk 140 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 591 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.049375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.039938 restraints weight = 146552.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041084 restraints weight = 88627.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041929 restraints weight = 62681.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042522 restraints weight = 48467.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042953 restraints weight = 40175.352| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19738 Z= 0.169 Angle : 0.797 12.450 27022 Z= 0.360 Chirality : 0.049 0.423 3368 Planarity : 0.005 0.096 3200 Dihedral : 13.520 102.833 5039 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.07 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.17), residues: 2181 helix: 0.32 (0.27), residues: 382 sheet: -1.35 (0.22), residues: 552 loop : -2.19 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 100J TYR 0.017 0.001 TYR D 586 PHE 0.019 0.001 PHE H 27 TRP 0.015 0.002 TRP E 96 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00368 (19574) covalent geometry : angle 0.72377 (26564) SS BOND : bond 0.00392 ( 34) SS BOND : angle 1.06235 ( 68) hydrogen bonds : bond 0.04102 ( 506) hydrogen bonds : angle 6.01321 ( 1329) link_ALPHA1-2 : bond 0.00563 ( 2) link_ALPHA1-2 : angle 2.41218 ( 6) link_ALPHA1-3 : bond 0.01189 ( 8) link_ALPHA1-3 : angle 1.91318 ( 24) link_ALPHA1-6 : bond 0.00755 ( 6) link_ALPHA1-6 : angle 2.31234 ( 18) link_BETA1-2 : bond 0.00685 ( 7) link_BETA1-2 : angle 2.03326 ( 21) link_BETA1-4 : bond 0.00639 ( 48) link_BETA1-4 : angle 2.54463 ( 144) link_BETA1-6 : bond 0.00618 ( 6) link_BETA1-6 : angle 1.57042 ( 18) link_NAG-ASN : bond 0.00531 ( 53) link_NAG-ASN : angle 3.44576 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.774 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: M 35 TYR cc_start: 0.8289 (m-10) cc_final: 0.7504 (m-10) REVERT: M 95 MET cc_start: 0.9080 (ttt) cc_final: 0.7374 (ttt) REVERT: M 97 GLN cc_start: 0.8343 (tp40) cc_final: 0.8043 (tm-30) REVERT: M 98 GLU cc_start: 0.7914 (tt0) cc_final: 0.7273 (tt0) REVERT: N 93 ASP cc_start: 0.8826 (t0) cc_final: 0.8445 (t0) REVERT: H 82 MET cc_start: 0.8841 (mmp) cc_final: 0.8620 (mmp) REVERT: L 14 THR cc_start: 0.7293 (m) cc_final: 0.6843 (m) REVERT: A 207 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9144 (tmtt) REVERT: A 302 ASN cc_start: 0.8489 (t0) cc_final: 0.8097 (t0) REVERT: A 368 ASP cc_start: 0.8586 (t0) cc_final: 0.8304 (t70) REVERT: A 482 GLU cc_start: 0.8030 (mp0) cc_final: 0.7830 (mp0) REVERT: B 530 MET cc_start: 0.7665 (mtp) cc_final: 0.6549 (mtm) REVERT: B 535 MET cc_start: 0.8114 (mpp) cc_final: 0.7793 (mpp) REVERT: B 647 GLU cc_start: 0.8966 (mp0) cc_final: 0.8716 (mp0) REVERT: C 104 MET cc_start: 0.9477 (ttm) cc_final: 0.9210 (ttm) REVERT: C 207 LYS cc_start: 0.9415 (mmtt) cc_final: 0.8658 (tmtt) REVERT: C 426 MET cc_start: 0.8763 (tpp) cc_final: 0.8414 (tpp) REVERT: E 95 MET cc_start: 0.9200 (ttp) cc_final: 0.8487 (ttm) REVERT: E 104 MET cc_start: 0.9384 (ttm) cc_final: 0.9089 (ttm) REVERT: E 477 ASP cc_start: 0.9567 (m-30) cc_final: 0.9024 (p0) REVERT: F 530 MET cc_start: 0.8163 (mtm) cc_final: 0.7853 (ppp) REVERT: F 584 GLU cc_start: 0.9080 (tt0) cc_final: 0.8849 (tm-30) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1595 time to fit residues: 38.4012 Evaluate side-chains 119 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 122 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.039542 restraints weight = 150882.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.040648 restraints weight = 92312.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041465 restraints weight = 65400.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.042019 restraints weight = 50911.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042391 restraints weight = 42574.078| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19738 Z= 0.210 Angle : 0.835 14.487 27022 Z= 0.376 Chirality : 0.049 0.428 3368 Planarity : 0.005 0.061 3200 Dihedral : 12.851 102.479 5039 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.55 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.17), residues: 2181 helix: 0.24 (0.27), residues: 388 sheet: -1.37 (0.21), residues: 565 loop : -2.18 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 476 TYR 0.015 0.001 TYR F 586 PHE 0.017 0.002 PHE A 53 TRP 0.023 0.002 TRP A 69 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00461 (19574) covalent geometry : angle 0.76385 (26564) SS BOND : bond 0.00281 ( 34) SS BOND : angle 0.92123 ( 68) hydrogen bonds : bond 0.04181 ( 506) hydrogen bonds : angle 6.00737 ( 1329) link_ALPHA1-2 : bond 0.00497 ( 2) link_ALPHA1-2 : angle 2.44558 ( 6) link_ALPHA1-3 : bond 0.01239 ( 8) link_ALPHA1-3 : angle 1.97006 ( 24) link_ALPHA1-6 : bond 0.00724 ( 6) link_ALPHA1-6 : angle 2.14647 ( 18) link_BETA1-2 : bond 0.00553 ( 7) link_BETA1-2 : angle 1.93331 ( 21) link_BETA1-4 : bond 0.00622 ( 48) link_BETA1-4 : angle 2.55717 ( 144) link_BETA1-6 : bond 0.00532 ( 6) link_BETA1-6 : angle 1.85401 ( 18) link_NAG-ASN : bond 0.00548 ( 53) link_NAG-ASN : angle 3.55253 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.792 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: M 35 TYR cc_start: 0.8245 (m-10) cc_final: 0.7570 (m-10) REVERT: M 95 MET cc_start: 0.9105 (ttt) cc_final: 0.8107 (ttt) REVERT: N 93 ASP cc_start: 0.8781 (t0) cc_final: 0.8469 (t0) REVERT: H 82 MET cc_start: 0.8789 (mmp) cc_final: 0.8568 (mmp) REVERT: H 100 ASP cc_start: 0.8196 (t0) cc_final: 0.7964 (t0) REVERT: A 142 MET cc_start: 0.8215 (mmm) cc_final: 0.7742 (mmm) REVERT: A 207 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9145 (tmtt) REVERT: A 302 ASN cc_start: 0.8527 (t0) cc_final: 0.8113 (t0) REVERT: A 368 ASP cc_start: 0.8601 (t0) cc_final: 0.8323 (t70) REVERT: B 530 MET cc_start: 0.7835 (mtp) cc_final: 0.6777 (mtm) REVERT: B 535 MET cc_start: 0.8118 (mpp) cc_final: 0.7731 (mpp) REVERT: B 647 GLU cc_start: 0.9011 (mp0) cc_final: 0.8762 (mp0) REVERT: D 530 MET cc_start: 0.7909 (pmm) cc_final: 0.7624 (mpp) REVERT: C 95 MET cc_start: 0.9021 (tpt) cc_final: 0.8805 (tpt) REVERT: C 104 MET cc_start: 0.9493 (ttm) cc_final: 0.9252 (ttm) REVERT: C 207 LYS cc_start: 0.9471 (mmtt) cc_final: 0.8698 (tmtt) REVERT: C 426 MET cc_start: 0.9075 (tpp) cc_final: 0.8755 (tpp) REVERT: E 95 MET cc_start: 0.9166 (ttp) cc_final: 0.8461 (ttm) REVERT: E 104 MET cc_start: 0.9322 (ttm) cc_final: 0.9060 (ttm) REVERT: E 477 ASP cc_start: 0.9601 (m-30) cc_final: 0.9020 (p0) REVERT: F 647 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8549 (mt-10) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1500 time to fit residues: 35.0423 Evaluate side-chains 116 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 174 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 185 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 591 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.039787 restraints weight = 148837.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040897 restraints weight = 90923.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.041700 restraints weight = 64198.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042260 restraints weight = 50086.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042663 restraints weight = 41831.206| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19738 Z= 0.188 Angle : 0.810 12.355 27022 Z= 0.363 Chirality : 0.049 0.427 3368 Planarity : 0.005 0.083 3200 Dihedral : 12.355 102.848 5039 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 2181 helix: 0.26 (0.27), residues: 389 sheet: -1.42 (0.21), residues: 584 loop : -2.12 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.018 0.001 TYR D 586 PHE 0.014 0.001 PHE E 53 TRP 0.019 0.002 TRP F 610 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00412 (19574) covalent geometry : angle 0.73939 (26564) SS BOND : bond 0.00504 ( 34) SS BOND : angle 0.96616 ( 68) hydrogen bonds : bond 0.04002 ( 506) hydrogen bonds : angle 5.85336 ( 1329) link_ALPHA1-2 : bond 0.00547 ( 2) link_ALPHA1-2 : angle 2.49063 ( 6) link_ALPHA1-3 : bond 0.01255 ( 8) link_ALPHA1-3 : angle 1.93472 ( 24) link_ALPHA1-6 : bond 0.00775 ( 6) link_ALPHA1-6 : angle 2.03650 ( 18) link_BETA1-2 : bond 0.00473 ( 7) link_BETA1-2 : angle 2.00272 ( 21) link_BETA1-4 : bond 0.00606 ( 48) link_BETA1-4 : angle 2.51293 ( 144) link_BETA1-6 : bond 0.00634 ( 6) link_BETA1-6 : angle 1.87273 ( 18) link_NAG-ASN : bond 0.00525 ( 53) link_NAG-ASN : angle 3.44105 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.837 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: M 35 TYR cc_start: 0.8232 (m-10) cc_final: 0.7761 (m-10) REVERT: M 95 MET cc_start: 0.8969 (ttt) cc_final: 0.8125 (ttt) REVERT: N 89 MET cc_start: 0.6592 (ttp) cc_final: 0.6338 (ttp) REVERT: N 93 ASP cc_start: 0.8827 (t0) cc_final: 0.8499 (t0) REVERT: H 100 ASP cc_start: 0.8223 (t0) cc_final: 0.7973 (t0) REVERT: L 27 GLU cc_start: 0.8192 (tt0) cc_final: 0.7842 (mt-10) REVERT: A 142 MET cc_start: 0.8209 (mmm) cc_final: 0.7850 (mmm) REVERT: A 207 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9137 (tmtt) REVERT: A 302 ASN cc_start: 0.8450 (t0) cc_final: 0.8024 (t0) REVERT: A 368 ASP cc_start: 0.8596 (t0) cc_final: 0.8320 (t70) REVERT: B 530 MET cc_start: 0.7712 (mtp) cc_final: 0.6692 (mtm) REVERT: B 535 MET cc_start: 0.8191 (mpp) cc_final: 0.7906 (mpp) REVERT: D 530 MET cc_start: 0.7880 (pmm) cc_final: 0.7586 (mpp) REVERT: C 95 MET cc_start: 0.9010 (tpt) cc_final: 0.8793 (tpt) REVERT: C 104 MET cc_start: 0.9502 (ttm) cc_final: 0.9229 (ttm) REVERT: C 161 MET cc_start: 0.9130 (tpp) cc_final: 0.8896 (tpp) REVERT: C 207 LYS cc_start: 0.9455 (mmtt) cc_final: 0.8683 (tmtt) REVERT: C 426 MET cc_start: 0.9000 (tpp) cc_final: 0.8477 (tpp) REVERT: E 95 MET cc_start: 0.9153 (ttp) cc_final: 0.8534 (ttm) REVERT: E 104 MET cc_start: 0.9357 (ttm) cc_final: 0.8950 (ttm) REVERT: E 477 ASP cc_start: 0.9631 (m-30) cc_final: 0.9039 (p0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1434 time to fit residues: 33.1177 Evaluate side-chains 116 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 151 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 63 optimal weight: 9.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.040532 restraints weight = 147298.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041667 restraints weight = 90147.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042483 restraints weight = 63946.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043069 restraints weight = 49800.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043453 restraints weight = 41466.536| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19738 Z= 0.125 Angle : 0.747 12.349 27022 Z= 0.333 Chirality : 0.048 0.408 3368 Planarity : 0.004 0.070 3200 Dihedral : 11.520 103.046 5039 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.18), residues: 2181 helix: 0.44 (0.27), residues: 392 sheet: -1.17 (0.21), residues: 568 loop : -1.96 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 419 TYR 0.016 0.001 TYR D 586 PHE 0.010 0.001 PHE C 223 TRP 0.025 0.001 TRP A 427 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00271 (19574) covalent geometry : angle 0.67698 (26564) SS BOND : bond 0.00261 ( 34) SS BOND : angle 0.88684 ( 68) hydrogen bonds : bond 0.03646 ( 506) hydrogen bonds : angle 5.60068 ( 1329) link_ALPHA1-2 : bond 0.00724 ( 2) link_ALPHA1-2 : angle 2.49907 ( 6) link_ALPHA1-3 : bond 0.01170 ( 8) link_ALPHA1-3 : angle 1.66237 ( 24) link_ALPHA1-6 : bond 0.00886 ( 6) link_ALPHA1-6 : angle 1.86510 ( 18) link_BETA1-2 : bond 0.00504 ( 7) link_BETA1-2 : angle 1.97788 ( 21) link_BETA1-4 : bond 0.00619 ( 48) link_BETA1-4 : angle 2.34110 ( 144) link_BETA1-6 : bond 0.00941 ( 6) link_BETA1-6 : angle 1.77580 ( 18) link_NAG-ASN : bond 0.00534 ( 53) link_NAG-ASN : angle 3.32329 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TYR cc_start: 0.7993 (m-10) cc_final: 0.7651 (m-10) REVERT: M 95 MET cc_start: 0.8909 (ttt) cc_final: 0.8223 (ttt) REVERT: M 98 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6953 (tm-30) REVERT: N 93 ASP cc_start: 0.8787 (t0) cc_final: 0.8362 (t0) REVERT: L 81 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7735 (pm20) REVERT: A 95 MET cc_start: 0.8432 (tpt) cc_final: 0.7923 (tpp) REVERT: A 142 MET cc_start: 0.8168 (mmm) cc_final: 0.7833 (mmm) REVERT: A 207 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9150 (tmtt) REVERT: A 302 ASN cc_start: 0.8580 (t0) cc_final: 0.8241 (t0) REVERT: A 368 ASP cc_start: 0.8580 (t0) cc_final: 0.8311 (t70) REVERT: B 530 MET cc_start: 0.7760 (mtp) cc_final: 0.6630 (mtm) REVERT: B 535 MET cc_start: 0.8271 (mpp) cc_final: 0.8044 (mpp) REVERT: B 642 ILE cc_start: 0.9739 (mt) cc_final: 0.9476 (tp) REVERT: B 647 GLU cc_start: 0.9082 (mp0) cc_final: 0.8778 (mp0) REVERT: D 530 MET cc_start: 0.7961 (pmm) cc_final: 0.7708 (mpp) REVERT: D 535 MET cc_start: 0.9302 (mpp) cc_final: 0.9023 (mpp) REVERT: C 104 MET cc_start: 0.9467 (ttm) cc_final: 0.9211 (ttm) REVERT: C 161 MET cc_start: 0.9124 (tpp) cc_final: 0.8859 (tpp) REVERT: C 207 LYS cc_start: 0.9452 (mmtt) cc_final: 0.8678 (tmtt) REVERT: C 426 MET cc_start: 0.9010 (tpp) cc_final: 0.8321 (tpp) REVERT: E 95 MET cc_start: 0.9197 (ttp) cc_final: 0.8568 (ttm) REVERT: E 104 MET cc_start: 0.9321 (ttm) cc_final: 0.8997 (ttm) REVERT: E 142 MET cc_start: 0.5923 (mmm) cc_final: 0.5081 (mpp) REVERT: E 477 ASP cc_start: 0.9583 (m-30) cc_final: 0.8986 (p0) REVERT: F 535 MET cc_start: 0.9205 (mtp) cc_final: 0.8862 (mpp) REVERT: F 575 GLN cc_start: 0.9397 (tt0) cc_final: 0.8959 (tm-30) REVERT: F 576 LEU cc_start: 0.9732 (tp) cc_final: 0.9325 (pp) REVERT: F 647 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8409 (pt0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1326 time to fit residues: 32.8771 Evaluate side-chains 120 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 1 optimal weight: 0.0370 chunk 148 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 135 optimal weight: 0.0060 chunk 128 optimal weight: 5.9990 chunk 183 optimal weight: 0.0020 chunk 199 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 591 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS F 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041852 restraints weight = 140573.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043071 restraints weight = 85219.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043972 restraints weight = 59709.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044568 restraints weight = 45900.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045020 restraints weight = 38023.341| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19738 Z= 0.116 Angle : 0.727 12.212 27022 Z= 0.325 Chirality : 0.048 0.381 3368 Planarity : 0.004 0.067 3200 Dihedral : 10.345 102.381 5039 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.18), residues: 2181 helix: 0.66 (0.28), residues: 381 sheet: -0.97 (0.21), residues: 577 loop : -1.88 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 480 TYR 0.028 0.001 TYR D 643 PHE 0.016 0.001 PHE L 98 TRP 0.026 0.001 TRP A 45 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00245 (19574) covalent geometry : angle 0.66036 (26564) SS BOND : bond 0.00236 ( 34) SS BOND : angle 0.78792 ( 68) hydrogen bonds : bond 0.03196 ( 506) hydrogen bonds : angle 5.27919 ( 1329) link_ALPHA1-2 : bond 0.00962 ( 2) link_ALPHA1-2 : angle 2.46587 ( 6) link_ALPHA1-3 : bond 0.01168 ( 8) link_ALPHA1-3 : angle 1.41632 ( 24) link_ALPHA1-6 : bond 0.01035 ( 6) link_ALPHA1-6 : angle 1.64951 ( 18) link_BETA1-2 : bond 0.00478 ( 7) link_BETA1-2 : angle 2.10885 ( 21) link_BETA1-4 : bond 0.00627 ( 48) link_BETA1-4 : angle 2.21875 ( 144) link_BETA1-6 : bond 0.01175 ( 6) link_BETA1-6 : angle 1.83314 ( 18) link_NAG-ASN : bond 0.00577 ( 53) link_NAG-ASN : angle 3.23252 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TYR cc_start: 0.7625 (m-10) cc_final: 0.7301 (m-10) REVERT: M 95 MET cc_start: 0.8856 (ttt) cc_final: 0.7884 (ttt) REVERT: M 98 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6267 (tm-30) REVERT: N 93 ASP cc_start: 0.8802 (t0) cc_final: 0.8439 (t0) REVERT: H 100 ASP cc_start: 0.8173 (t70) cc_final: 0.7914 (t0) REVERT: L 33 LEU cc_start: 0.9090 (tp) cc_final: 0.8876 (tp) REVERT: A 142 MET cc_start: 0.8243 (mmm) cc_final: 0.7947 (mmm) REVERT: A 207 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9065 (tmtt) REVERT: A 368 ASP cc_start: 0.8502 (t0) cc_final: 0.8253 (t0) REVERT: A 482 GLU cc_start: 0.8242 (mp0) cc_final: 0.8003 (mp0) REVERT: B 530 MET cc_start: 0.7724 (mtp) cc_final: 0.6567 (mtm) REVERT: B 642 ILE cc_start: 0.9762 (mt) cc_final: 0.9501 (tp) REVERT: B 647 GLU cc_start: 0.8890 (mp0) cc_final: 0.8662 (mp0) REVERT: D 530 MET cc_start: 0.7787 (pmm) cc_final: 0.7582 (mpp) REVERT: C 94 ASN cc_start: 0.8899 (t0) cc_final: 0.8627 (t0) REVERT: C 207 LYS cc_start: 0.9443 (mmtt) cc_final: 0.8680 (tmtt) REVERT: C 426 MET cc_start: 0.8937 (tpp) cc_final: 0.8192 (tpp) REVERT: E 95 MET cc_start: 0.9138 (ttp) cc_final: 0.8451 (ttp) REVERT: E 104 MET cc_start: 0.9291 (ttm) cc_final: 0.8952 (ttm) REVERT: E 142 MET cc_start: 0.6309 (mmm) cc_final: 0.5361 (mpp) REVERT: E 161 MET cc_start: 0.8772 (tpt) cc_final: 0.8513 (tpp) REVERT: E 477 ASP cc_start: 0.9588 (m-30) cc_final: 0.8855 (p0) REVERT: F 530 MET cc_start: 0.8463 (mpp) cc_final: 0.7698 (mmp) REVERT: F 535 MET cc_start: 0.9181 (mtp) cc_final: 0.8793 (mpp) REVERT: F 575 GLN cc_start: 0.9377 (tt0) cc_final: 0.9078 (tm-30) REVERT: F 576 LEU cc_start: 0.9727 (tp) cc_final: 0.9510 (pp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1398 time to fit residues: 39.6756 Evaluate side-chains 128 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 174 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041275 restraints weight = 145534.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042410 restraints weight = 89542.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043246 restraints weight = 63555.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043809 restraints weight = 49488.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044246 restraints weight = 41245.714| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19738 Z= 0.130 Angle : 0.732 12.299 27022 Z= 0.324 Chirality : 0.047 0.388 3368 Planarity : 0.004 0.051 3200 Dihedral : 10.123 101.379 5039 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.18), residues: 2181 helix: 0.71 (0.28), residues: 383 sheet: -0.94 (0.22), residues: 578 loop : -1.86 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 542 TYR 0.023 0.001 TYR D 586 PHE 0.011 0.001 PHE E 382 TRP 0.024 0.001 TRP A 427 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00286 (19574) covalent geometry : angle 0.66700 (26564) SS BOND : bond 0.00212 ( 34) SS BOND : angle 0.72568 ( 68) hydrogen bonds : bond 0.03253 ( 506) hydrogen bonds : angle 5.24949 ( 1329) link_ALPHA1-2 : bond 0.00874 ( 2) link_ALPHA1-2 : angle 2.50136 ( 6) link_ALPHA1-3 : bond 0.01088 ( 8) link_ALPHA1-3 : angle 1.50643 ( 24) link_ALPHA1-6 : bond 0.00868 ( 6) link_ALPHA1-6 : angle 1.65539 ( 18) link_BETA1-2 : bond 0.00397 ( 7) link_BETA1-2 : angle 1.93269 ( 21) link_BETA1-4 : bond 0.00548 ( 48) link_BETA1-4 : angle 2.21641 ( 144) link_BETA1-6 : bond 0.01002 ( 6) link_BETA1-6 : angle 1.76767 ( 18) link_NAG-ASN : bond 0.00481 ( 53) link_NAG-ASN : angle 3.21197 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 35 TYR cc_start: 0.7740 (m-10) cc_final: 0.7137 (m-10) REVERT: M 95 MET cc_start: 0.8902 (ttt) cc_final: 0.7977 (ttt) REVERT: N 93 ASP cc_start: 0.8707 (t0) cc_final: 0.8342 (t0) REVERT: H 95 MET cc_start: 0.6345 (mtm) cc_final: 0.6123 (mtp) REVERT: H 100 ASP cc_start: 0.8313 (t70) cc_final: 0.8057 (t0) REVERT: A 95 MET cc_start: 0.8564 (tpt) cc_final: 0.7884 (tpp) REVERT: A 142 MET cc_start: 0.8134 (mmm) cc_final: 0.7787 (mmm) REVERT: A 207 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9078 (tmtt) REVERT: A 368 ASP cc_start: 0.8521 (t0) cc_final: 0.8273 (t0) REVERT: B 530 MET cc_start: 0.7783 (mtp) cc_final: 0.6639 (mtm) REVERT: B 535 MET cc_start: 0.8009 (mpp) cc_final: 0.7725 (mpp) REVERT: B 642 ILE cc_start: 0.9781 (mt) cc_final: 0.9554 (tp) REVERT: B 647 GLU cc_start: 0.8886 (mp0) cc_final: 0.8683 (mp0) REVERT: C 207 LYS cc_start: 0.9455 (mmtt) cc_final: 0.8705 (tmtt) REVERT: C 426 MET cc_start: 0.8830 (tpp) cc_final: 0.8159 (tpp) REVERT: E 95 MET cc_start: 0.9101 (ttp) cc_final: 0.8504 (ttm) REVERT: E 104 MET cc_start: 0.9162 (ttm) cc_final: 0.8929 (ttm) REVERT: E 142 MET cc_start: 0.6043 (mmm) cc_final: 0.5005 (mpp) REVERT: E 161 MET cc_start: 0.8809 (tpt) cc_final: 0.8438 (tpt) REVERT: E 477 ASP cc_start: 0.9595 (m-30) cc_final: 0.8840 (p0) REVERT: F 535 MET cc_start: 0.9224 (mtp) cc_final: 0.8821 (mpp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1350 time to fit residues: 33.5397 Evaluate side-chains 114 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 94 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040992 restraints weight = 142188.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042192 restraints weight = 86156.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043039 restraints weight = 60370.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.043651 restraints weight = 46627.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.044084 restraints weight = 38626.452| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19738 Z= 0.127 Angle : 0.740 12.598 27022 Z= 0.327 Chirality : 0.047 0.388 3368 Planarity : 0.004 0.050 3200 Dihedral : 9.906 101.910 5039 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 2181 helix: 0.69 (0.28), residues: 384 sheet: -0.87 (0.22), residues: 574 loop : -1.83 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.021 0.001 TYR D 586 PHE 0.009 0.001 PHE E 382 TRP 0.051 0.002 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00281 (19574) covalent geometry : angle 0.67510 (26564) SS BOND : bond 0.00205 ( 34) SS BOND : angle 1.16211 ( 68) hydrogen bonds : bond 0.03357 ( 506) hydrogen bonds : angle 5.24988 ( 1329) link_ALPHA1-2 : bond 0.00964 ( 2) link_ALPHA1-2 : angle 2.49661 ( 6) link_ALPHA1-3 : bond 0.01090 ( 8) link_ALPHA1-3 : angle 1.43574 ( 24) link_ALPHA1-6 : bond 0.00879 ( 6) link_ALPHA1-6 : angle 1.62525 ( 18) link_BETA1-2 : bond 0.00385 ( 7) link_BETA1-2 : angle 1.87301 ( 21) link_BETA1-4 : bond 0.00555 ( 48) link_BETA1-4 : angle 2.19809 ( 144) link_BETA1-6 : bond 0.00981 ( 6) link_BETA1-6 : angle 1.77282 ( 18) link_NAG-ASN : bond 0.00478 ( 53) link_NAG-ASN : angle 3.19306 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 29 PHE cc_start: 0.8497 (t80) cc_final: 0.8102 (t80) REVERT: M 35 TYR cc_start: 0.7786 (m-10) cc_final: 0.7268 (m-10) REVERT: M 95 MET cc_start: 0.8849 (ttt) cc_final: 0.8033 (ttt) REVERT: N 89 MET cc_start: 0.6113 (ttp) cc_final: 0.4595 (ttp) REVERT: N 93 ASP cc_start: 0.8708 (t0) cc_final: 0.8317 (t0) REVERT: H 100 ASP cc_start: 0.8414 (t70) cc_final: 0.8139 (t0) REVERT: L 33 LEU cc_start: 0.9038 (tp) cc_final: 0.8797 (tp) REVERT: A 95 MET cc_start: 0.8563 (tpt) cc_final: 0.7864 (tpp) REVERT: A 142 MET cc_start: 0.8122 (mmm) cc_final: 0.7796 (mmm) REVERT: A 207 LYS cc_start: 0.9470 (mmtt) cc_final: 0.8991 (tptp) REVERT: A 368 ASP cc_start: 0.8540 (t0) cc_final: 0.8293 (t0) REVERT: B 530 MET cc_start: 0.7780 (mtp) cc_final: 0.6594 (mtm) REVERT: B 535 MET cc_start: 0.8091 (mpp) cc_final: 0.7780 (mpp) REVERT: B 642 ILE cc_start: 0.9771 (mt) cc_final: 0.9508 (tp) REVERT: D 530 MET cc_start: 0.7990 (pmm) cc_final: 0.7478 (mpp) REVERT: C 207 LYS cc_start: 0.9441 (mmtt) cc_final: 0.8664 (tmtt) REVERT: C 426 MET cc_start: 0.8835 (tpp) cc_final: 0.8237 (tpp) REVERT: E 95 MET cc_start: 0.9078 (ttp) cc_final: 0.8489 (ttm) REVERT: E 104 MET cc_start: 0.9233 (ttm) cc_final: 0.8972 (ttm) REVERT: E 142 MET cc_start: 0.6233 (mmm) cc_final: 0.5294 (mpp) REVERT: E 161 MET cc_start: 0.8790 (tpt) cc_final: 0.8434 (tpt) REVERT: E 477 ASP cc_start: 0.9605 (m-30) cc_final: 0.8837 (p0) REVERT: F 535 MET cc_start: 0.9196 (mtp) cc_final: 0.8804 (mpp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1338 time to fit residues: 30.9614 Evaluate side-chains 116 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 136 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 195 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS F 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.038856 restraints weight = 150037.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.039943 restraints weight = 92193.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.040739 restraints weight = 65192.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041271 restraints weight = 50682.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041680 restraints weight = 42300.415| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19738 Z= 0.286 Angle : 0.911 13.189 27022 Z= 0.413 Chirality : 0.050 0.426 3368 Planarity : 0.005 0.059 3200 Dihedral : 10.675 101.264 5039 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.08 (0.17), residues: 2181 helix: 0.10 (0.26), residues: 386 sheet: -1.22 (0.21), residues: 570 loop : -1.99 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 542 TYR 0.019 0.002 TYR F 586 PHE 0.023 0.002 PHE A 53 TRP 0.041 0.003 TRP C 479 HIS 0.005 0.002 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00621 (19574) covalent geometry : angle 0.85060 (26564) SS BOND : bond 0.00315 ( 34) SS BOND : angle 1.25063 ( 68) hydrogen bonds : bond 0.04362 ( 506) hydrogen bonds : angle 5.81335 ( 1329) link_ALPHA1-2 : bond 0.00221 ( 2) link_ALPHA1-2 : angle 2.41427 ( 6) link_ALPHA1-3 : bond 0.01105 ( 8) link_ALPHA1-3 : angle 1.85664 ( 24) link_ALPHA1-6 : bond 0.00567 ( 6) link_ALPHA1-6 : angle 2.00419 ( 18) link_BETA1-2 : bond 0.00587 ( 7) link_BETA1-2 : angle 1.89223 ( 21) link_BETA1-4 : bond 0.00616 ( 48) link_BETA1-4 : angle 2.48576 ( 144) link_BETA1-6 : bond 0.00912 ( 6) link_BETA1-6 : angle 1.99462 ( 18) link_NAG-ASN : bond 0.00538 ( 53) link_NAG-ASN : angle 3.41612 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.48 seconds wall clock time: 47 minutes 51.37 seconds (2871.37 seconds total)