Starting phenix.real_space_refine on Sun Sep 13 00:32:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.map" model { file = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_9062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mar_9062/09_2026/6mar_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.15, per 1000 atoms: 0.22 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: 2.22 Conformation dependent library (CDL) restraints added in 859.3 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: 0.50 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: 3.58 Time building geometry restraints manager: 2.71 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 - 14.98: 10152 14.98 - 29.96: 455 29.96 - 44.94: 121 44.94 - 59.92: 15 59.92 - 74.90: 7 Dihedral angle restraints: 10750 sinusoidal: 4354 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 10747 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: 2.840 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.480 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 9.477 74.900 6524 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/Z covalent geometry : bond 0.00742 / 0.36 (19574) covalent geometry : angle 1.03990 / 0.51 (26564) SS BOND : bond 0.00444 / 0.25 ( 34) SS BOND : angle 1.23033 / 0.84 ( 68) hydrogen bonds : bond 0.23938 / 15.91 ( 506) hydrogen bonds : angle 8.48111 / 5.61 ( 1329) link_ALPHA1-2 : bond 0.00260 / 0.13 ( 2) link_ALPHA1-2 : angle 2.21363 / 1.05 ( 6) link_ALPHA1-3 : bond 0.00471 / 0.19 ( 8) link_ALPHA1-3 : angle 2.28952 / 1.30 ( 24) link_ALPHA1-6 : bond 0.00519 / 0.29 ( 6) link_ALPHA1-6 : angle 2.36274 / 1.33 ( 18) link_BETA1-2 : bond 0.00992 / 0.67 ( 7) link_BETA1-2 : angle 2.72807 / 1.59 ( 21) link_BETA1-4 : bond 0.00936 / 0.61 ( 48) link_BETA1-4 : angle 3.89151 / 2.44 ( 144) link_BETA1-6 : bond 0.00329 / 0.16 ( 6) link_BETA1-6 : angle 1.91254 / 1.11 ( 18) link_NAG-ASN : bond 0.00753 / 0.46 ( 53) link_NAG-ASN : angle 4.81789 / 3.18 ( 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 : 0.758 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: 0.7148 (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: 0.6644 (mtm) cc_final: 0.6290 (ptp) REVERT: D 586 TYR cc_start: 0.9352 (t80) cc_final: 0.8919 (t80) REVERT: D 589 ASP cc_start: 0.8582 (m-30) cc_final: 0.8291 (p0) REVERT: C 45 TRP cc_start: 0.8840 (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: 0.1602 time to fit residues: 66.2428 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 : 0.696 ------------------------------------------------------------------------------- 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... 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 = 0.3144 r_free = 0.3144 target = 0.050579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041164 restraints weight = 141582.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042360 restraints weight = 85141.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.043223 restraints weight = 59480.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.043825 restraints weight = 45865.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044236 restraints weight = 37894.860| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1793 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= 0.141 Angle : 0.785 12.803 27022 Z= 0.363 Chirality : 0.047 0.411 3368 Planarity : 0.005 0.065 3200 Dihedral : 6.042 43.252 2387 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.84 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -2.64 (0.17), residues: 2181 helix: -0.36 (0.25), residues: 393 sheet: -1.47 (0.21), residues: 568 loop : -2.44 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 429 TYR 0.023 0.001 TYR D 643 PHE 0.018 0.002 PHE A 53 TRP 0.018 0.002 TRP B 614 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19574) covalent geometry : angle 0.70611 / 0.35 (26564) SS BOND : bond 0.00385 / 0.24 ( 34) SS BOND : angle 1.05435 / 0.63 ( 68) hydrogen bonds : bond 0.04653 / 3.03 ( 506) hydrogen bonds : angle 6.53178 / 4.34 ( 1329) link_ALPHA1-2 : bond 0.00308 / 0.16 ( 2) link_ALPHA1-2 : angle 1.90979 / 0.93 ( 6) link_ALPHA1-3 : bond 0.00892 / 0.41 ( 8) link_ALPHA1-3 : angle 2.07233 / 1.25 ( 24) link_ALPHA1-6 : bond 0.00562 / 0.26 ( 6) link_ALPHA1-6 : angle 2.17598 / 1.29 ( 18) link_BETA1-2 : bond 0.00439 / 0.20 ( 7) link_BETA1-2 : angle 2.53844 / 1.53 ( 21) link_BETA1-4 : bond 0.00695 / 0.43 ( 48) link_BETA1-4 : angle 2.39094 / 1.49 ( 144) link_BETA1-6 : bond 0.00410 / 0.19 ( 6) link_BETA1-6 : angle 1.26314 / 0.73 ( 18) link_NAG-ASN : bond 0.00588 / 0.36 ( 53) link_NAG-ASN : angle 3.64700 / 2.45 ( 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 211 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.640 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: M 35 TYR cc_start: 0.8542 (m-10) cc_final: 0.8331 (m-10) REVERT: M 95 MET cc_start: 0.8727 (ttt) cc_final: 0.8468 (ttt) REVERT: M 100 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7877 (mtp-110) REVERT: N 93 ASP cc_start: 0.8818 (t0) cc_final: 0.8450 (t0) REVERT: H 100 ASP cc_start: 0.8250 (t0) cc_final: 0.7961 (t0) REVERT: A 95 MET cc_start: 0.8648 (tpp) cc_final: 0.8411 (tpp) REVERT: A 207 LYS cc_start: 0.9493 (mmtt) cc_final: 0.9194 (tmtt) REVERT: A 211 GLU cc_start: 0.9128 (tt0) cc_final: 0.8822 (tm-30) REVERT: A 302 ASN cc_start: 0.8390 (t0) cc_final: 0.8162 (t0) REVERT: A 368 ASP cc_start: 0.8569 (t0) cc_final: 0.8220 (t0) REVERT: B 530 MET cc_start: 0.7679 (mtp) cc_final: 0.6562 (mtm) REVERT: B 535 MET cc_start: 0.7785 (mpp) cc_final: 0.7508 (mpp) REVERT: B 543 ASN cc_start: 0.9307 (m-40) cc_final: 0.8954 (m110) REVERT: D 564 HIS cc_start: 0.7509 (t-90) cc_final: 0.7295 (t-170) REVERT: D 655 LYS cc_start: 0.9155 (mptt) cc_final: 0.8947 (pttp) REVERT: C 45 TRP cc_start: 0.8860 (m-10) cc_final: 0.8323 (m-90) REVERT: C 207 LYS cc_start: 0.9377 (mmtt) cc_final: 0.8739 (tmtt) REVERT: E 104 MET cc_start: 0.9282 (ttm) cc_final: 0.9007 (ttm) REVERT: E 161 MET cc_start: 0.8642 (tpt) cc_final: 0.8422 (tpt) REVERT: E 420 ILE cc_start: 0.8715 (mt) cc_final: 0.8464 (tt) REVERT: E 434 MET cc_start: 0.9236 (tmm) cc_final: 0.8953 (tmm) REVERT: E 477 ASP cc_start: 0.9540 (m-30) cc_final: 0.9053 (p0) REVERT: F 575 GLN cc_start: 0.9433 (tt0) cc_final: 0.8967 (tm-30) REVERT: F 647 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8653 (mt-10) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1465 time to fit residues: 46.7908 Evaluate side-chains 134 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 9.9990 chunk 119 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 170 GLN A 478 ASN B 591 GLN B 640 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 330 HIS C 422 GLN F 652 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.039755 restraints weight = 148231.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040924 restraints weight = 89185.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041757 restraints weight = 62618.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042351 restraints weight = 48343.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042758 restraints weight = 40054.928| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19738 Z= 0.223 Angle : 0.842 13.128 27022 Z= 0.388 Chirality : 0.048 0.406 3368 Planarity : 0.005 0.064 3200 Dihedral : 5.906 43.958 2387 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.95 % Favored : 90.00 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % 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: -2.41 (0.17), residues: 2181 helix: 0.21 (0.27), residues: 383 sheet: -1.46 (0.21), residues: 577 loop : -2.34 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 77 TYR 0.015 0.002 TYR F 586 PHE 0.021 0.002 PHE A 53 TRP 0.018 0.002 TRP F 614 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (19574) covalent geometry : angle 0.77378 / 0.37 (26564) SS BOND : bond 0.00415 / 0.19 ( 34) SS BOND : angle 0.94904 / 0.63 ( 68) hydrogen bonds : bond 0.04610 / 3.01 ( 506) hydrogen bonds : angle 6.26578 / 4.18 ( 1329) link_ALPHA1-2 : bond 0.00162 / 0.08 ( 2) link_ALPHA1-2 : angle 1.63791 / 0.82 ( 6) link_ALPHA1-3 : bond 0.00905 / 0.41 ( 8) link_ALPHA1-3 : angle 1.94055 / 1.20 ( 24) link_ALPHA1-6 : bond 0.00413 / 0.21 ( 6) link_ALPHA1-6 : angle 2.11351 / 1.27 ( 18) link_BETA1-2 : bond 0.00452 / 0.25 ( 7) link_BETA1-2 : angle 2.38379 / 1.44 ( 21) link_BETA1-4 : bond 0.00654 / 0.41 ( 48) link_BETA1-4 : angle 2.46329 / 1.51 ( 144) link_BETA1-6 : bond 0.00357 / 0.14 ( 6) link_BETA1-6 : angle 1.31523 / 0.75 ( 18) link_NAG-ASN : bond 0.00533 / 0.35 ( 53) link_NAG-ASN : angle 3.52294 / 2.37 ( 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 162 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.767 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: 0.8454 (m-10) cc_final: 0.7398 (m-10) REVERT: M 95 MET cc_start: 0.8974 (ttt) cc_final: 0.7938 (ttt) REVERT: N 93 ASP cc_start: 0.8798 (t0) cc_final: 0.8499 (t0) REVERT: H 100 ASP cc_start: 0.8359 (t0) cc_final: 0.8127 (t0) REVERT: A 142 MET cc_start: 0.7692 (mmm) cc_final: 0.7339 (mmm) REVERT: A 207 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9190 (tmtt) REVERT: A 302 ASN cc_start: 0.8449 (t0) cc_final: 0.8138 (t0) REVERT: A 368 ASP cc_start: 0.8613 (t0) cc_final: 0.8350 (t0) REVERT: B 530 MET cc_start: 0.7713 (mtp) cc_final: 0.6499 (mtm) REVERT: B 535 MET cc_start: 0.8059 (mpp) cc_final: 0.7746 (mpp) REVERT: C 104 MET cc_start: 0.9443 (ttm) cc_final: 0.9168 (ttm) REVERT: C 207 LYS cc_start: 0.9433 (mmtt) cc_final: 0.8771 (tmtt) REVERT: E 104 MET cc_start: 0.9373 (ttm) cc_final: 0.9020 (ttm) REVERT: E 477 ASP cc_start: 0.9545 (m-30) cc_final: 0.9039 (p0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1634 time to fit residues: 39.9079 Evaluate side-chains 122 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 9.9990 chunk 161 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 179 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN B 591 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.040425 restraints weight = 144698.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041619 restraints weight = 86954.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042462 restraints weight = 60732.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.043005 restraints weight = 46841.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043446 restraints weight = 39314.837| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2631 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= 0.144 Angle : 0.736 11.243 27022 Z= 0.339 Chirality : 0.047 0.393 3368 Planarity : 0.005 0.094 3200 Dihedral : 5.508 41.489 2387 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -2.15 (0.17), residues: 2181 helix: 0.41 (0.27), residues: 381 sheet: -1.26 (0.22), residues: 552 loop : -2.18 (0.17), residues: 1248 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 0.021 0.001 PHE H 27 TRP 0.016 0.002 TRP E 96 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19574) covalent geometry : angle 0.66733 / 0.32 (26564) SS BOND : bond 0.00281 / 0.15 ( 34) SS BOND : angle 1.05003 / 0.69 ( 68) hydrogen bonds : bond 0.03903 / 2.55 ( 506) hydrogen bonds : angle 5.87391 / 3.92 ( 1329) link_ALPHA1-2 : bond 0.00229 / 0.12 ( 2) link_ALPHA1-2 : angle 1.69613 / 0.84 ( 6) link_ALPHA1-3 : bond 0.00727 / 0.34 ( 8) link_ALPHA1-3 : angle 1.83524 / 1.13 ( 24) link_ALPHA1-6 : bond 0.00516 / 0.24 ( 6) link_ALPHA1-6 : angle 1.93349 / 1.16 ( 18) link_BETA1-2 : bond 0.00316 / 0.15 ( 7) link_BETA1-2 : angle 2.21182 / 1.35 ( 21) link_BETA1-4 : bond 0.00611 / 0.38 ( 48) link_BETA1-4 : angle 2.21683 / 1.36 ( 144) link_BETA1-6 : bond 0.00424 / 0.19 ( 6) link_BETA1-6 : angle 1.18523 / 0.69 ( 18) link_NAG-ASN : bond 0.00515 / 0.33 ( 53) link_NAG-ASN : angle 3.28570 / 2.18 ( 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 165 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.682 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: M 35 TYR cc_start: 0.8221 (m-10) cc_final: 0.7375 (m-10) REVERT: M 95 MET cc_start: 0.9023 (ttt) cc_final: 0.7307 (ttt) REVERT: N 93 ASP cc_start: 0.8824 (t0) cc_final: 0.8410 (t0) REVERT: H 82 MET cc_start: 0.8833 (mmp) cc_final: 0.8617 (mmp) REVERT: L 14 THR cc_start: 0.7364 (m) cc_final: 0.6888 (m) REVERT: A 207 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9155 (tmtt) REVERT: A 302 ASN cc_start: 0.8462 (t0) cc_final: 0.8087 (t0) REVERT: A 368 ASP cc_start: 0.8601 (t0) cc_final: 0.8325 (t70) REVERT: B 530 MET cc_start: 0.7711 (mtp) cc_final: 0.6714 (mtm) REVERT: B 535 MET cc_start: 0.8070 (mpp) cc_final: 0.7773 (mpp) REVERT: B 647 GLU cc_start: 0.8931 (mp0) cc_final: 0.8676 (mp0) REVERT: D 535 MET cc_start: 0.8999 (mtm) cc_final: 0.8792 (mpp) REVERT: D 564 HIS cc_start: 0.7586 (t-90) cc_final: 0.7379 (t-170) REVERT: C 95 MET cc_start: 0.9090 (tpt) cc_final: 0.8828 (tpt) REVERT: C 104 MET cc_start: 0.9475 (ttm) cc_final: 0.9157 (ttm) REVERT: C 207 LYS cc_start: 0.9409 (mmtt) cc_final: 0.8713 (tmtt) REVERT: E 95 MET cc_start: 0.9202 (ttp) cc_final: 0.8491 (ttm) REVERT: E 104 MET cc_start: 0.9355 (ttm) cc_final: 0.9060 (ttm) REVERT: E 142 MET cc_start: 0.5479 (mmm) cc_final: 0.4576 (mpp) REVERT: E 477 ASP cc_start: 0.9577 (m-30) cc_final: 0.9025 (p0) REVERT: F 530 MET cc_start: 0.8168 (mtm) cc_final: 0.7857 (ppp) REVERT: F 584 GLU cc_start: 0.9077 (tt0) cc_final: 0.8823 (tm-30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1597 time to fit residues: 40.0860 Evaluate side-chains 124 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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: 9.9990 chunk 142 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.1980 chunk 152 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 181 optimal weight: 0.4980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 17 GLN L 90 GLN A 170 GLN A 478 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.049562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040276 restraints weight = 148921.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.041406 restraints weight = 90979.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042243 restraints weight = 64459.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042796 restraints weight = 50139.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043192 restraints weight = 41897.405| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19738 Z= 0.164 Angle : 0.743 10.775 27022 Z= 0.340 Chirality : 0.047 0.392 3368 Planarity : 0.004 0.075 3200 Dihedral : 5.370 40.169 2387 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.03 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -2.07 (0.18), residues: 2181 helix: 0.46 (0.27), residues: 385 sheet: -1.26 (0.21), residues: 577 loop : -2.10 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 273 TYR 0.014 0.001 TYR D 586 PHE 0.014 0.001 PHE E 53 TRP 0.019 0.002 TRP A 69 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (19574) covalent geometry : angle 0.67869 / 0.33 (26564) SS BOND : bond 0.00255 / 0.14 ( 34) SS BOND : angle 0.88362 / 0.58 ( 68) hydrogen bonds : bond 0.03877 / 2.53 ( 506) hydrogen bonds : angle 5.78839 / 3.87 ( 1329) link_ALPHA1-2 : bond 0.00187 / 0.10 ( 2) link_ALPHA1-2 : angle 1.63647 / 0.81 ( 6) link_ALPHA1-3 : bond 0.00829 / 0.43 ( 8) link_ALPHA1-3 : angle 1.78441 / 1.10 ( 24) link_ALPHA1-6 : bond 0.00453 / 0.23 ( 6) link_ALPHA1-6 : angle 1.92947 / 1.16 ( 18) link_BETA1-2 : bond 0.00287 / 0.14 ( 7) link_BETA1-2 : angle 2.27974 / 1.37 ( 21) link_BETA1-4 : bond 0.00615 / 0.38 ( 48) link_BETA1-4 : angle 2.25966 / 1.39 ( 144) link_BETA1-6 : bond 0.00321 / 0.15 ( 6) link_BETA1-6 : angle 1.21103 / 0.69 ( 18) link_NAG-ASN : bond 0.00527 / 0.35 ( 53) link_NAG-ASN : angle 3.18715 / 2.12 ( 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 161 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.888 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: 0.8128 (m-10) cc_final: 0.7469 (m-10) REVERT: M 95 MET cc_start: 0.8803 (ttt) cc_final: 0.6970 (ttt) REVERT: N 93 ASP cc_start: 0.8779 (t0) cc_final: 0.8450 (t0) REVERT: H 82 MET cc_start: 0.8786 (mmp) cc_final: 0.8559 (mmp) REVERT: H 100 ASP cc_start: 0.8106 (t0) cc_final: 0.7849 (t0) REVERT: A 142 MET cc_start: 0.8220 (mmm) cc_final: 0.7848 (mmm) REVERT: A 207 LYS cc_start: 0.9480 (mmtt) cc_final: 0.9132 (tmtt) REVERT: A 302 ASN cc_start: 0.8400 (t0) cc_final: 0.7997 (t0) REVERT: A 368 ASP cc_start: 0.8584 (t0) cc_final: 0.8318 (t0) REVERT: B 530 MET cc_start: 0.7692 (mtp) cc_final: 0.6554 (mtm) REVERT: B 535 MET cc_start: 0.8074 (mpp) cc_final: 0.7794 (mpp) REVERT: B 647 GLU cc_start: 0.8965 (mp0) cc_final: 0.8758 (mp0) REVERT: D 535 MET cc_start: 0.9044 (mtm) cc_final: 0.8808 (mpp) REVERT: C 95 MET cc_start: 0.9213 (tpt) cc_final: 0.8892 (tpt) REVERT: C 104 MET cc_start: 0.9510 (ttm) cc_final: 0.9216 (ttm) REVERT: C 161 MET cc_start: 0.9147 (tpp) cc_final: 0.8922 (tpp) REVERT: C 207 LYS cc_start: 0.9434 (mmtt) cc_final: 0.8663 (tmtt) REVERT: C 426 MET cc_start: 0.8827 (tpp) cc_final: 0.8616 (tpp) REVERT: E 95 MET cc_start: 0.9162 (ttp) cc_final: 0.8392 (ttm) REVERT: E 104 MET cc_start: 0.9217 (ttm) cc_final: 0.9009 (ttm) REVERT: E 142 MET cc_start: 0.5973 (mmm) cc_final: 0.5293 (mpp) REVERT: E 477 ASP cc_start: 0.9604 (m-30) cc_final: 0.9038 (p0) REVERT: F 584 GLU cc_start: 0.9072 (tt0) cc_final: 0.8849 (tm-30) REVERT: F 588 ARG cc_start: 0.8891 (tmm-80) cc_final: 0.8523 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1635 time to fit residues: 40.1090 Evaluate side-chains 122 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.039632 restraints weight = 146087.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.040793 restraints weight = 88348.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041642 restraints weight = 62001.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.042226 restraints weight = 47907.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.042616 restraints weight = 39794.238| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19738 Z= 0.190 Angle : 0.780 15.172 27022 Z= 0.355 Chirality : 0.047 0.397 3368 Planarity : 0.005 0.108 3200 Dihedral : 5.450 39.504 2387 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -2.10 (0.17), residues: 2181 helix: 0.35 (0.27), residues: 392 sheet: -1.29 (0.21), residues: 579 loop : -2.10 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 94 TYR 0.016 0.001 TYR D 586 PHE 0.015 0.002 PHE A 53 TRP 0.019 0.002 TRP A 427 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (19574) covalent geometry : angle 0.71419 / 0.34 (26564) SS BOND : bond 0.00289 / 0.17 ( 34) SS BOND : angle 0.93023 / 0.62 ( 68) hydrogen bonds : bond 0.03904 / 2.54 ( 506) hydrogen bonds : angle 5.77397 / 3.86 ( 1329) link_ALPHA1-2 : bond 0.00156 / 0.08 ( 2) link_ALPHA1-2 : angle 1.63241 / 0.81 ( 6) link_ALPHA1-3 : bond 0.00795 / 0.40 ( 8) link_ALPHA1-3 : angle 1.78508 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00457 / 0.24 ( 6) link_ALPHA1-6 : angle 1.93404 / 1.16 ( 18) link_BETA1-2 : bond 0.00299 / 0.14 ( 7) link_BETA1-2 : angle 2.19200 / 1.32 ( 21) link_BETA1-4 : bond 0.00559 / 0.35 ( 48) link_BETA1-4 : angle 2.23237 / 1.38 ( 144) link_BETA1-6 : bond 0.00280 / 0.13 ( 6) link_BETA1-6 : angle 1.26188 / 0.71 ( 18) link_NAG-ASN : bond 0.00493 / 0.32 ( 53) link_NAG-ASN : angle 3.37805 / 2.24 ( 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 154 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.793 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: M 35 TYR cc_start: 0.8149 (m-10) cc_final: 0.7775 (m-10) REVERT: M 95 MET cc_start: 0.8874 (ttt) cc_final: 0.8023 (ttt) REVERT: N 93 ASP cc_start: 0.8763 (t0) cc_final: 0.8411 (t0) REVERT: H 95 MET cc_start: 0.7500 (mtp) cc_final: 0.7224 (mtp) REVERT: H 100 ASP cc_start: 0.8268 (t0) cc_final: 0.8006 (t0) REVERT: H 101 ASP cc_start: 0.7752 (t0) cc_final: 0.6933 (p0) REVERT: L 81 GLU cc_start: 0.8584 (tp30) cc_final: 0.7699 (pm20) REVERT: A 142 MET cc_start: 0.8118 (mmm) cc_final: 0.7761 (mmm) REVERT: A 207 LYS cc_start: 0.9507 (mmtt) cc_final: 0.9144 (tmtt) REVERT: A 211 GLU cc_start: 0.9111 (tt0) cc_final: 0.8803 (tm-30) REVERT: A 302 ASN cc_start: 0.8392 (t0) cc_final: 0.7991 (t0) REVERT: A 368 ASP cc_start: 0.8603 (t0) cc_final: 0.8327 (t70) REVERT: B 530 MET cc_start: 0.7624 (mtp) cc_final: 0.6598 (mtm) REVERT: B 535 MET cc_start: 0.8090 (mpp) cc_final: 0.7702 (mpp) REVERT: C 95 MET cc_start: 0.9238 (tpt) cc_final: 0.8928 (tpt) REVERT: C 104 MET cc_start: 0.9501 (ttm) cc_final: 0.9221 (ttm) REVERT: C 207 LYS cc_start: 0.9439 (mmtt) cc_final: 0.8648 (tmtt) REVERT: C 426 MET cc_start: 0.8939 (tpp) cc_final: 0.8621 (tpp) REVERT: E 95 MET cc_start: 0.9191 (ttp) cc_final: 0.8461 (ttm) REVERT: E 104 MET cc_start: 0.9342 (ttm) cc_final: 0.8975 (ttm) REVERT: E 142 MET cc_start: 0.5979 (mmm) cc_final: 0.5348 (mpp) REVERT: E 477 ASP cc_start: 0.9602 (m-30) cc_final: 0.9032 (p0) REVERT: F 584 GLU cc_start: 0.9070 (tt0) cc_final: 0.8849 (tm-30) REVERT: F 588 ARG cc_start: 0.8936 (tmm-80) cc_final: 0.8525 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1509 time to fit residues: 35.7749 Evaluate side-chains 123 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 97 GLN L 90 GLN A 170 GLN B 651 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.039100 restraints weight = 148269.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.040243 restraints weight = 89428.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041071 restraints weight = 62689.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.041650 restraints weight = 48477.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042036 restraints weight = 40286.062| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19738 Z= 0.215 Angle : 0.808 13.905 27022 Z= 0.370 Chirality : 0.048 0.406 3368 Planarity : 0.005 0.058 3200 Dihedral : 5.541 39.215 2387 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.05 % Allowed : 1.23 % 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: -2.19 (0.17), residues: 2181 helix: 0.23 (0.27), residues: 388 sheet: -1.39 (0.21), residues: 581 loop : -2.09 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 100F TYR 0.021 0.002 TYR D 586 PHE 0.018 0.002 PHE A 53 TRP 0.026 0.002 TRP A 427 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (19574) covalent geometry : angle 0.74763 / 0.36 (26564) SS BOND : bond 0.00270 / 0.17 ( 34) SS BOND : angle 0.91111 / 0.62 ( 68) hydrogen bonds : bond 0.04184 / 2.74 ( 506) hydrogen bonds : angle 5.82618 / 3.89 ( 1329) link_ALPHA1-2 : bond 0.00124 / 0.06 ( 2) link_ALPHA1-2 : angle 1.66648 / 0.82 ( 6) link_ALPHA1-3 : bond 0.00753 / 0.36 ( 8) link_ALPHA1-3 : angle 1.79908 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00456 / 0.26 ( 6) link_ALPHA1-6 : angle 2.00271 / 1.20 ( 18) link_BETA1-2 : bond 0.00318 / 0.15 ( 7) link_BETA1-2 : angle 2.16669 / 1.30 ( 21) link_BETA1-4 : bond 0.00568 / 0.35 ( 48) link_BETA1-4 : angle 2.26399 / 1.40 ( 144) link_BETA1-6 : bond 0.00325 / 0.13 ( 6) link_BETA1-6 : angle 1.31172 / 0.74 ( 18) link_NAG-ASN : bond 0.00493 / 0.33 ( 53) link_NAG-ASN : angle 3.28220 / 2.18 ( 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 150 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 35 TYR cc_start: 0.8162 (m-10) cc_final: 0.7746 (m-10) REVERT: M 95 MET cc_start: 0.8986 (ttt) cc_final: 0.8498 (ttt) REVERT: N 93 ASP cc_start: 0.8808 (t0) cc_final: 0.8445 (t0) REVERT: H 100 ASP cc_start: 0.8230 (t0) cc_final: 0.7982 (t0) REVERT: L 81 GLU cc_start: 0.8596 (tp30) cc_final: 0.7803 (pm20) REVERT: A 142 MET cc_start: 0.8168 (mmm) cc_final: 0.7827 (mmm) REVERT: A 207 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9156 (tmtt) REVERT: A 302 ASN cc_start: 0.8651 (t0) cc_final: 0.8286 (t0) REVERT: A 368 ASP cc_start: 0.8579 (t0) cc_final: 0.8300 (t70) REVERT: B 530 MET cc_start: 0.7673 (mtp) cc_final: 0.6548 (mtm) REVERT: B 642 ILE cc_start: 0.9753 (mt) cc_final: 0.9490 (tp) REVERT: B 647 GLU cc_start: 0.9154 (mp0) cc_final: 0.8803 (mp0) REVERT: D 535 MET cc_start: 0.9264 (mpp) cc_final: 0.9017 (mpp) REVERT: C 104 MET cc_start: 0.9493 (ttm) cc_final: 0.9220 (ttm) REVERT: C 161 MET cc_start: 0.9135 (tpp) cc_final: 0.8894 (tpp) REVERT: C 207 LYS cc_start: 0.9455 (mmtt) cc_final: 0.8626 (tmtt) REVERT: C 426 MET cc_start: 0.9011 (tpp) cc_final: 0.8657 (tpp) REVERT: E 95 MET cc_start: 0.9208 (ttp) cc_final: 0.8458 (ttm) REVERT: E 104 MET cc_start: 0.9390 (ttm) cc_final: 0.8973 (ttm) REVERT: E 477 ASP cc_start: 0.9621 (m-30) cc_final: 0.9041 (p0) REVERT: F 588 ARG cc_start: 0.8918 (tmm-80) cc_final: 0.8500 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1425 time to fit residues: 33.4816 Evaluate side-chains 121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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: 0.0040 chunk 148 optimal weight: 1.9990 chunk 194 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 0.0370 chunk 183 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.041157 restraints weight = 144572.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.042349 restraints weight = 88200.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043202 restraints weight = 62198.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043817 restraints weight = 48212.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.044224 restraints weight = 40014.586| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3442 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= 0.116 Angle : 0.716 12.455 27022 Z= 0.324 Chirality : 0.047 0.377 3368 Planarity : 0.004 0.049 3200 Dihedral : 5.010 33.363 2387 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % 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 : 0.00 % 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: -1.76 (0.18), residues: 2181 helix: 0.75 (0.27), residues: 380 sheet: -1.03 (0.22), residues: 561 loop : -1.92 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.017 0.001 TYR D 586 PHE 0.012 0.001 PHE N 71 TRP 0.029 0.001 TRP A 45 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (19574) covalent geometry : angle 0.65205 / 0.31 (26564) SS BOND : bond 0.00393 / 0.27 ( 34) SS BOND : angle 0.91594 / 0.57 ( 68) hydrogen bonds : bond 0.03455 / 2.24 ( 506) hydrogen bonds : angle 5.35874 / 3.59 ( 1329) link_ALPHA1-2 : bond 0.00383 / 0.20 ( 2) link_ALPHA1-2 : angle 1.69796 / 0.84 ( 6) link_ALPHA1-3 : bond 0.00836 / 0.42 ( 8) link_ALPHA1-3 : angle 1.63997 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00683 / 0.30 ( 6) link_ALPHA1-6 : angle 1.81134 / 1.07 ( 18) link_BETA1-2 : bond 0.00408 / 0.20 ( 7) link_BETA1-2 : angle 2.10573 / 1.27 ( 21) link_BETA1-4 : bond 0.00643 / 0.39 ( 48) link_BETA1-4 : angle 1.94942 / 1.22 ( 144) link_BETA1-6 : bond 0.00488 / 0.24 ( 6) link_BETA1-6 : angle 1.12103 / 0.67 ( 18) link_NAG-ASN : bond 0.00597 / 0.37 ( 53) link_NAG-ASN : angle 3.25579 / 2.15 ( 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 166 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 29 PHE cc_start: 0.8305 (t80) cc_final: 0.8002 (t80) REVERT: M 35 TYR cc_start: 0.7624 (m-10) cc_final: 0.7114 (m-10) REVERT: M 95 MET cc_start: 0.8924 (ttt) cc_final: 0.7655 (ttt) REVERT: N 74 ARG cc_start: 0.8721 (tpt170) cc_final: 0.8438 (tmm160) REVERT: N 93 ASP cc_start: 0.8779 (t0) cc_final: 0.8356 (t0) REVERT: L 81 GLU cc_start: 0.8398 (tp30) cc_final: 0.7784 (pm20) REVERT: A 95 MET cc_start: 0.8224 (tpt) cc_final: 0.7802 (tpp) REVERT: A 207 LYS cc_start: 0.9487 (mmtt) cc_final: 0.9128 (tmtt) REVERT: A 302 ASN cc_start: 0.8602 (t0) cc_final: 0.8254 (t0) REVERT: A 368 ASP cc_start: 0.8549 (t0) cc_final: 0.8291 (t0) REVERT: B 530 MET cc_start: 0.7376 (mtp) cc_final: 0.6303 (mtm) REVERT: B 535 MET cc_start: 0.8158 (mpp) cc_final: 0.7852 (mpp) REVERT: B 588 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8716 (tpp80) REVERT: B 642 ILE cc_start: 0.9760 (mt) cc_final: 0.9492 (tp) REVERT: C 207 LYS cc_start: 0.9436 (mmtt) cc_final: 0.8650 (tmtt) REVERT: C 426 MET cc_start: 0.8761 (tpp) cc_final: 0.8293 (tpp) REVERT: E 95 MET cc_start: 0.9169 (ttp) cc_final: 0.8493 (ttm) REVERT: E 104 MET cc_start: 0.9335 (ttm) cc_final: 0.9069 (ttm) REVERT: E 161 MET cc_start: 0.8763 (tpt) cc_final: 0.8512 (tpp) REVERT: E 477 ASP cc_start: 0.9580 (m-30) cc_final: 0.8945 (p0) REVERT: F 535 MET cc_start: 0.9207 (mtp) cc_final: 0.8831 (mpp) REVERT: F 575 GLN cc_start: 0.9403 (tt0) cc_final: 0.8977 (tm-30) REVERT: F 576 LEU cc_start: 0.9715 (tp) cc_final: 0.9308 (pp) REVERT: F 588 ARG cc_start: 0.8864 (tmm-80) cc_final: 0.8408 (tmm-80) REVERT: F 589 ASP cc_start: 0.9047 (m-30) cc_final: 0.8845 (m-30) REVERT: F 647 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8358 (pt0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1416 time to fit residues: 36.9661 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 : 0.721 ------------------------------------------------------------------------------- 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: 8.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 97 GLN A 170 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN F 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.049405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.040000 restraints weight = 145423.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041169 restraints weight = 88529.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.042015 restraints weight = 62289.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042588 restraints weight = 48202.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043016 restraints weight = 40072.185| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19738 Z= 0.164 Angle : 0.741 12.275 27022 Z= 0.338 Chirality : 0.046 0.383 3368 Planarity : 0.004 0.065 3200 Dihedral : 5.104 32.257 2387 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.05 % Allowed : 0.61 % 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: -1.86 (0.18), residues: 2181 helix: 0.70 (0.28), residues: 383 sheet: -1.16 (0.21), residues: 600 loop : -1.97 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 77 TYR 0.017 0.001 TYR D 586 PHE 0.014 0.001 PHE A 53 TRP 0.029 0.002 TRP A 427 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (19574) covalent geometry : angle 0.68163 / 0.32 (26564) SS BOND : bond 0.00216 / 0.13 ( 34) SS BOND : angle 0.80281 / 0.52 ( 68) hydrogen bonds : bond 0.03686 / 2.38 ( 506) hydrogen bonds : angle 5.45826 / 3.65 ( 1329) link_ALPHA1-2 : bond 0.00188 / 0.10 ( 2) link_ALPHA1-2 : angle 1.59960 / 0.79 ( 6) link_ALPHA1-3 : bond 0.00697 / 0.33 ( 8) link_ALPHA1-3 : angle 1.68398 / 1.05 ( 24) link_ALPHA1-6 : bond 0.00457 / 0.22 ( 6) link_ALPHA1-6 : angle 1.82964 / 1.10 ( 18) link_BETA1-2 : bond 0.00243 / 0.11 ( 7) link_BETA1-2 : angle 2.06082 / 1.24 ( 21) link_BETA1-4 : bond 0.00547 / 0.34 ( 48) link_BETA1-4 : angle 2.04577 / 1.28 ( 144) link_BETA1-6 : bond 0.00325 / 0.15 ( 6) link_BETA1-6 : angle 1.20900 / 0.69 ( 18) link_NAG-ASN : bond 0.00474 / 0.31 ( 53) link_NAG-ASN : angle 3.15055 / 2.08 ( 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 : 0.840 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: M 29 PHE cc_start: 0.8493 (t80) cc_final: 0.8155 (t80) REVERT: M 35 TYR cc_start: 0.7887 (m-10) cc_final: 0.7418 (m-10) REVERT: M 95 MET cc_start: 0.8864 (ttt) cc_final: 0.7849 (ttt) REVERT: N 93 ASP cc_start: 0.8771 (t0) cc_final: 0.8366 (t0) REVERT: H 100 ASP cc_start: 0.8042 (t0) cc_final: 0.7819 (t0) REVERT: L 81 GLU cc_start: 0.8482 (tp30) cc_final: 0.7799 (pm20) REVERT: A 95 MET cc_start: 0.8476 (tpt) cc_final: 0.7837 (tpp) REVERT: A 142 MET cc_start: 0.8055 (mmm) cc_final: 0.7670 (mmm) REVERT: A 207 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9142 (tmtt) REVERT: A 302 ASN cc_start: 0.8632 (t0) cc_final: 0.8257 (t0) REVERT: A 368 ASP cc_start: 0.8578 (t0) cc_final: 0.8319 (t0) REVERT: B 530 MET cc_start: 0.7498 (mtp) cc_final: 0.6387 (mtm) REVERT: B 535 MET cc_start: 0.8041 (mpp) cc_final: 0.7733 (mpp) REVERT: B 642 ILE cc_start: 0.9729 (mt) cc_final: 0.9477 (tp) REVERT: C 95 MET cc_start: 0.9026 (tpt) cc_final: 0.8756 (tpt) REVERT: C 426 MET cc_start: 0.8921 (tpp) cc_final: 0.8476 (tpp) REVERT: E 95 MET cc_start: 0.9179 (ttp) cc_final: 0.8558 (ttm) REVERT: E 104 MET cc_start: 0.9242 (ttm) cc_final: 0.8923 (ttm) REVERT: E 142 MET cc_start: 0.5117 (mmm) cc_final: 0.4061 (mpp) REVERT: E 161 MET cc_start: 0.8759 (tpt) cc_final: 0.8403 (tpt) REVERT: E 477 ASP cc_start: 0.9597 (m-30) cc_final: 0.8959 (p0) REVERT: F 535 MET cc_start: 0.9224 (mtp) cc_final: 0.8837 (mpp) REVERT: F 542 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8155 (mmp80) REVERT: F 588 ARG cc_start: 0.8926 (tmm-80) cc_final: 0.8445 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1379 time to fit residues: 33.5060 Evaluate side-chains 121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 8.9990 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 478 ASN ** 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 = 0.3141 r_free = 0.3141 target = 0.050502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.041063 restraints weight = 142577.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042250 restraints weight = 86935.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043107 restraints weight = 61223.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043699 restraints weight = 47431.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044119 restraints weight = 39392.274| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19738 Z= 0.112 Angle : 0.703 11.771 27022 Z= 0.319 Chirality : 0.046 0.373 3368 Planarity : 0.004 0.049 3200 Dihedral : 4.907 34.005 2387 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.71 (0.18), residues: 2181 helix: 0.82 (0.28), residues: 380 sheet: -1.05 (0.21), residues: 593 loop : -1.87 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 588 TYR 0.019 0.001 TYR D 586 PHE 0.017 0.001 PHE E 383 TRP 0.029 0.002 TRP A 45 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19574) covalent geometry : angle 0.64290 / 0.31 (26564) SS BOND : bond 0.00229 / 0.12 ( 34) SS BOND : angle 1.17129 / 0.75 ( 68) hydrogen bonds : bond 0.03375 / 2.18 ( 506) hydrogen bonds : angle 5.27669 / 3.53 ( 1329) link_ALPHA1-2 : bond 0.00314 / 0.16 ( 2) link_ALPHA1-2 : angle 1.63597 / 0.80 ( 6) link_ALPHA1-3 : bond 0.00752 / 0.36 ( 8) link_ALPHA1-3 : angle 1.61357 / 0.99 ( 24) link_ALPHA1-6 : bond 0.00579 / 0.25 ( 6) link_ALPHA1-6 : angle 1.74231 / 1.03 ( 18) link_BETA1-2 : bond 0.00295 / 0.14 ( 7) link_BETA1-2 : angle 1.93292 / 1.16 ( 21) link_BETA1-4 : bond 0.00584 / 0.36 ( 48) link_BETA1-4 : angle 1.92310 / 1.21 ( 144) link_BETA1-6 : bond 0.00420 / 0.20 ( 6) link_BETA1-6 : angle 1.08845 / 0.64 ( 18) link_NAG-ASN : bond 0.00516 / 0.32 ( 53) link_NAG-ASN : angle 3.07004 / 2.01 ( 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 156 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 29 PHE cc_start: 0.8464 (t80) cc_final: 0.8222 (t80) REVERT: M 35 TYR cc_start: 0.7625 (m-10) cc_final: 0.7051 (m-10) REVERT: M 82 MET cc_start: 0.9287 (mpp) cc_final: 0.9083 (mpp) REVERT: M 95 MET cc_start: 0.8806 (ttt) cc_final: 0.7644 (ttt) REVERT: N 93 ASP cc_start: 0.8746 (t0) cc_final: 0.8352 (t0) REVERT: L 81 GLU cc_start: 0.8351 (tp30) cc_final: 0.7807 (pm20) REVERT: A 95 MET cc_start: 0.8398 (tpt) cc_final: 0.7779 (tpp) REVERT: A 142 MET cc_start: 0.7989 (mmm) cc_final: 0.7786 (mmm) REVERT: A 207 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9070 (tmtt) REVERT: A 302 ASN cc_start: 0.8647 (t0) cc_final: 0.8297 (t0) REVERT: A 368 ASP cc_start: 0.8573 (t0) cc_final: 0.8319 (t0) REVERT: A 482 GLU cc_start: 0.8297 (mp0) cc_final: 0.8089 (mp0) REVERT: B 530 MET cc_start: 0.7439 (mtp) cc_final: 0.6301 (mtm) REVERT: B 535 MET cc_start: 0.8162 (mpp) cc_final: 0.7857 (mpp) REVERT: B 642 ILE cc_start: 0.9713 (mt) cc_final: 0.9462 (tp) REVERT: C 193 LEU cc_start: 0.9109 (mm) cc_final: 0.8748 (tp) REVERT: C 207 LYS cc_start: 0.9471 (mmtt) cc_final: 0.8648 (tmtt) REVERT: C 426 MET cc_start: 0.8735 (tpp) cc_final: 0.8347 (tpp) REVERT: E 95 MET cc_start: 0.9148 (ttp) cc_final: 0.8573 (ttm) REVERT: E 104 MET cc_start: 0.9219 (ttm) cc_final: 0.8999 (ttm) REVERT: E 142 MET cc_start: 0.5249 (mmm) cc_final: 0.3889 (mpp) REVERT: E 161 MET cc_start: 0.8780 (tpt) cc_final: 0.8410 (tpt) REVERT: E 477 ASP cc_start: 0.9597 (m-30) cc_final: 0.8844 (p0) REVERT: F 535 MET cc_start: 0.9191 (mtp) cc_final: 0.8821 (mpp) REVERT: F 575 GLN cc_start: 0.9341 (tt0) cc_final: 0.8954 (tm-30) REVERT: F 576 LEU cc_start: 0.9713 (tp) cc_final: 0.9329 (pp) REVERT: F 588 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8433 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1459 time to fit residues: 35.6222 Evaluate side-chains 121 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 478 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** 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 = 0.3076 r_free = 0.3076 target = 0.048384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.039201 restraints weight = 149585.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.040317 restraints weight = 91714.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041110 restraints weight = 64990.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041673 restraints weight = 50542.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.042040 restraints weight = 42078.431| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19738 Z= 0.251 Angle : 0.858 12.339 27022 Z= 0.394 Chirality : 0.049 0.401 3368 Planarity : 0.005 0.061 3200 Dihedral : 5.463 30.876 2387 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % 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 : 0.05 % 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: -2.01 (0.17), residues: 2181 helix: 0.34 (0.27), residues: 382 sheet: -1.22 (0.21), residues: 568 loop : -2.00 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 61 TYR 0.017 0.002 TYR F 586 PHE 0.023 0.002 PHE A 53 TRP 0.037 0.003 TRP A 427 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (19574) covalent geometry : angle 0.80471 / 0.38 (26564) SS BOND : bond 0.00295 / 0.18 ( 34) SS BOND : angle 1.25178 / 0.80 ( 68) hydrogen bonds : bond 0.04245 / 2.79 ( 506) hydrogen bonds : angle 5.74205 / 3.86 ( 1329) link_ALPHA1-2 : bond 0.00156 / 0.07 ( 2) link_ALPHA1-2 : angle 1.57799 / 0.78 ( 6) link_ALPHA1-3 : bond 0.00601 / 0.27 ( 8) link_ALPHA1-3 : angle 1.80324 / 1.12 ( 24) link_ALPHA1-6 : bond 0.00455 / 0.29 ( 6) link_ALPHA1-6 : angle 1.90040 / 1.16 ( 18) link_BETA1-2 : bond 0.00451 / 0.24 ( 7) link_BETA1-2 : angle 2.12150 / 1.27 ( 21) link_BETA1-4 : bond 0.00562 / 0.35 ( 48) link_BETA1-4 : angle 2.23846 / 1.40 ( 144) link_BETA1-6 : bond 0.00378 / 0.14 ( 6) link_BETA1-6 : angle 1.35500 / 0.76 ( 18) link_NAG-ASN : bond 0.00533 / 0.36 ( 53) link_NAG-ASN : angle 3.15042 / 2.08 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2648.84 seconds wall clock time: 47 minutes 9.75 seconds (2829.75 seconds total)