Starting phenix.real_space_refine on Sat Jul 4 05:23:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3q_29708/07_2026/8g3q_29708.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11520 2.51 5 N 3120 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18618 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "G" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "F" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "D" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 986 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "a" 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: "b" 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: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" 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: "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: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "l" 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: "n" 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: "o" 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: "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: 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: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "t" 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: "v" 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: "w" 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: "1" 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: "2" 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: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "4" 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: "6" 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: "7" 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: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.23 Number of scatterers: 18618 At special positions: 0 Unit cell: (134.48, 136.12, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3864 8.00 N 3120 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.04 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=1.98 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.08 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.05 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.04 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.07 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.16 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.05 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.06 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.01 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.07 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.06 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.07 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.04 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.12 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=1.99 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.06 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.07 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.08 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.05 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.06 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.07 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=1.99 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.06 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.07 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.07 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.04 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS F 337 " distance=2.08 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 447 " distance=2.14 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 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 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " NAG-ASN " NAG 1 1 " - " ASN H 86 " " NAG 2 1 " - " ASN H 146 " " NAG 3 1 " - " ASN H 200 " " NAG 4 1 " - " ASN H 234 " " NAG 6 1 " - " ASN H 329 " " NAG 7 1 " - " ASN H 367 " " NAG a 1 " - " ASN E 86 " " NAG b 1 " - " ASN E 146 " " NAG c 1 " - " ASN E 200 " " NAG d 1 " - " ASN E 234 " " NAG f 1 " - " ASN E 329 " " NAG g 1 " - " ASN E 367 " " NAG i 1 " - " ASN F 86 " " NAG j 1 " - " ASN F 146 " " NAG k 1 " - " ASN F 200 " " NAG l 1 " - " ASN F 234 " " NAG n 1 " - " ASN F 329 " " NAG o 1 " - " ASN F 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 572.5 milliseconds 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4098 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 42 sheets defined 3.4% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.747A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.835A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.668A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.673A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.021A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.466A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.288A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 352 through 356 removed outlier: 4.381A pdb=" N TRP E 352 " --> pdb=" O GLY E 363 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.288A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.313A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.432A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.071A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.680A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.676A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.040A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.467A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.289A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.384A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.498A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.696A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.674A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.012A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.461A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.308A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.389A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.287A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.330A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.441A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.675A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG F 420 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.667A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 172 " --> pdb=" O MET F 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 184 removed outlier: 3.993A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 207 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU F 211 " --> pdb=" O TYR F 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 6.455A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 283 removed outlier: 5.285A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 352 through 356 removed outlier: 4.419A pdb=" N TRP F 352 " --> pdb=" O GLY F 363 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.316A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.484A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.082A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.500A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.492A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASN C 117 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.475A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.575A pdb=" N ASN I 117 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.509A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.505A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 57 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.550A pdb=" N ASN A 117 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 104 through 105 613 hydrogen bonds defined for protein. 1581 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: 3.52 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3243 1.31 - 1.44: 5080 1.44 - 1.57: 10556 1.57 - 1.69: 0 1.69 - 1.82: 134 Bond restraints: 19013 Sorted by residual: bond pdb=" N GLY F 286 " pdb=" CA GLY F 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.73e+01 bond pdb=" CA SER H 457 " pdb=" CB SER H 457 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.69e-02 3.50e+03 1.73e+01 bond pdb=" C SER H 88 " pdb=" O SER H 88 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.26e-02 6.30e+03 1.70e+01 bond pdb=" CA SER H 384 " pdb=" CB SER H 384 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.45e-02 4.76e+03 1.69e+01 bond pdb=" C PRO H 166 " pdb=" O PRO H 166 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.18e-02 7.18e+03 1.67e+01 ... (remaining 19008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 23579 2.95 - 5.90: 2142 5.90 - 8.84: 82 8.84 - 11.79: 3 11.79 - 14.74: 3 Bond angle restraints: 25809 Sorted by residual: angle pdb=" CG ARG A 106 " pdb=" CD ARG A 106 " pdb=" NE ARG A 106 " ideal model delta sigma weight residual 112.00 126.74 -14.74 2.20e+00 2.07e-01 4.49e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.81 106.10 5.71 8.60e-01 1.35e+00 4.40e+01 angle pdb=" OD1 ASN H 294 " pdb=" CG ASN H 294 " pdb=" ND2 ASN H 294 " ideal model delta sigma weight residual 122.60 129.21 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CG ARG I 106 " pdb=" CD ARG I 106 " pdb=" NE ARG I 106 " ideal model delta sigma weight residual 112.00 126.39 -14.39 2.20e+00 2.07e-01 4.28e+01 angle pdb=" CG ARG C 106 " pdb=" CD ARG C 106 " pdb=" NE ARG C 106 " ideal model delta sigma weight residual 112.00 126.32 -14.32 2.20e+00 2.07e-01 4.24e+01 ... (remaining 25804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9884 17.99 - 35.97: 581 35.97 - 53.96: 109 53.96 - 71.94: 25 71.94 - 89.92: 26 Dihedral angle restraints: 10625 sinusoidal: 4190 harmonic: 6435 Sorted by residual: dihedral pdb=" CA ALA C 9 " pdb=" C ALA C 9 " pdb=" N GLU C 10 " pdb=" CA GLU C 10 " ideal model delta harmonic sigma weight residual 180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY B 57 " pdb=" C GLY B 57 " pdb=" N VAL B 58 " pdb=" CA VAL B 58 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" N CYS A 96 " pdb=" CA CYS A 96 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 10622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1659 0.069 - 0.138: 1029 0.138 - 0.208: 328 0.208 - 0.277: 62 0.277 - 0.346: 7 Chirality restraints: 3085 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.82e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.84e+01 chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.54e+01 ... (remaining 3082 not shown) Planarity restraints: 3215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 281 " 0.079 2.00e-02 2.50e+03 4.26e-02 3.62e+01 pdb=" CG TYR E 281 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 281 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 281 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR E 281 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR E 281 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 281 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 281 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 281 " -0.080 2.00e-02 2.50e+03 4.16e-02 3.46e+01 pdb=" CG TYR F 281 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR F 281 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR F 281 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR F 281 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 281 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 281 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 281 " -0.076 2.00e-02 2.50e+03 4.00e-02 3.20e+01 pdb=" CG TYR H 281 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR H 281 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR H 281 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 281 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR H 281 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 281 " -0.056 2.00e-02 2.50e+03 ... (remaining 3212 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2089 2.76 - 3.29: 18605 3.29 - 3.83: 34654 3.83 - 4.36: 45039 4.36 - 4.90: 71580 Nonbonded interactions: 171967 Sorted by model distance: nonbonded pdb=" O ASP H 293 " pdb="CA CA H2000 " model vdw 2.222 2.510 nonbonded pdb=" OD2 ASP F 324 " pdb="CA CA F2000 " model vdw 2.233 2.510 nonbonded pdb=" O ASP G 293 " pdb="CA CA G2000 " model vdw 2.251 2.510 nonbonded pdb=" O GLY H 345 " pdb="CA CA H2000 " model vdw 2.257 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.257 2.510 ... (remaining 171962 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 '1' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 82 through 501) selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.910 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9372 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 : 0.014 0.126 19146 Z= 0.965 Angle : 1.756 14.760 26166 Z= 1.090 Chirality : 0.092 0.346 3085 Planarity : 0.011 0.079 3191 Dihedral : 13.033 89.925 6401 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.16 % Favored : 96.44 % Rotamer: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.16), residues: 2246 helix: -1.22 (0.94), residues: 24 sheet: -0.26 (0.16), residues: 885 loop : -0.83 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.003 ARG H 430 TYR 0.080 0.015 TYR F 281 PHE 0.049 0.012 PHE E 446 TRP 0.076 0.014 TRP H 178 HIS 0.019 0.006 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.01418 / 0.96 (19013) covalent geometry : angle 1.70521 / 1.09 (25809) SS BOND : bond 0.04590 / 3.12 ( 42) SS BOND : angle 2.40278 / 1.80 ( 84) hydrogen bonds : bond 0.15963 / 11.05 ( 592) hydrogen bonds : angle 8.99901 / 6.35 ( 1581) link_ALPHA1-2 : bond 0.01068 / 0.49 ( 4) link_ALPHA1-2 : angle 4.53907 / 2.59 ( 12) link_ALPHA1-3 : bond 0.01404 / 0.84 ( 8) link_ALPHA1-3 : angle 3.01526 / 1.82 ( 24) link_ALPHA1-6 : bond 0.00621 / 0.33 ( 8) link_ALPHA1-6 : angle 2.39425 / 1.50 ( 24) link_BETA1-4 : bond 0.01607 / 0.98 ( 47) link_BETA1-4 : angle 4.43032 / 3.17 ( 141) link_NAG-ASN : bond 0.02081 / 1.25 ( 24) link_NAG-ASN : angle 5.03337 / 3.22 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 178 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.9173 (p-90) REVERT: H 150 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8210 (tpt90) REVERT: F 178 TRP cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (p-90) REVERT: B 17 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 10 GLU cc_start: 0.8802 (tp30) cc_final: 0.8220 (tp30) REVERT: C 43 GLN cc_start: 0.8894 (mt0) cc_final: 0.8569 (mm-40) REVERT: D 59 PRO cc_start: 0.9517 (Cg_exo) cc_final: 0.9139 (Cg_endo) REVERT: L 2 ILE cc_start: 0.8154 (mt) cc_final: 0.7948 (mt) REVERT: L 17 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8750 (mp0) REVERT: L 54 ARG cc_start: 0.9238 (mtm-85) cc_final: 0.8954 (mtm-85) REVERT: L 81 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8738 (mt-10) REVERT: L 98 THR cc_start: 0.9194 (m) cc_final: 0.8726 (p) REVERT: A 23 LYS cc_start: 0.8942 (tttt) cc_final: 0.8668 (tttp) REVERT: A 81 MET cc_start: 0.9229 (ttp) cc_final: 0.9028 (ttp) outliers start: 4 outliers final: 0 residues processed: 273 average time/residue: 0.6924 time to fit residues: 209.0488 Evaluate side-chains 233 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 TRP Chi-restraints excluded: chain F residue 178 TRP 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: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN G 147 ASN H 147 ASN B 6 GLN D 27 GLN A 31 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.057217 restraints weight = 31474.895| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.49 r_work: 0.2603 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19146 Z= 0.181 Angle : 0.712 7.501 26166 Z= 0.367 Chirality : 0.047 0.163 3085 Planarity : 0.004 0.043 3191 Dihedral : 6.093 31.724 2468 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.80 % Favored : 97.02 % Rotamer: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2246 helix: -1.15 (0.59), residues: 24 sheet: -0.10 (0.18), residues: 821 loop : -0.23 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 24 TYR 0.018 0.002 TYR L 91 PHE 0.016 0.002 PHE G 410 TRP 0.023 0.002 TRP H 178 HIS 0.004 0.001 HIS F 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (19013) covalent geometry : angle 0.68266 / 0.36 (25809) SS BOND : bond 0.00387 / 0.21 ( 42) SS BOND : angle 0.70506 / 0.53 ( 84) hydrogen bonds : bond 0.04933 / 3.33 ( 592) hydrogen bonds : angle 7.50740 / 5.33 ( 1581) link_ALPHA1-2 : bond 0.00454 / 0.22 ( 4) link_ALPHA1-2 : angle 1.57425 / 0.83 ( 12) link_ALPHA1-3 : bond 0.00585 / 0.36 ( 8) link_ALPHA1-3 : angle 1.53700 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00419 / 0.23 ( 8) link_ALPHA1-6 : angle 1.19808 / 0.76 ( 24) link_BETA1-4 : bond 0.00346 / 0.20 ( 47) link_BETA1-4 : angle 2.08488 / 1.44 ( 141) link_NAG-ASN : bond 0.00339 / 0.18 ( 24) link_NAG-ASN : angle 2.57962 / 1.73 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 150 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7845 (mtp-110) REVERT: H 151 ASP cc_start: 0.8765 (p0) cc_final: 0.8536 (p0) REVERT: B 17 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8107 (mm-30) REVERT: B 24 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7935 (ttm-80) REVERT: B 39 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8223 (mmmm) REVERT: B 59 PRO cc_start: 0.9088 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 81 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8635 (tm-30) REVERT: B 82 ASP cc_start: 0.9196 (m-30) cc_final: 0.8829 (m-30) REVERT: C 43 GLN cc_start: 0.8583 (mt0) cc_final: 0.8269 (mm-40) REVERT: C 98 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (ttt-90) REVERT: D 59 PRO cc_start: 0.9165 (Cg_exo) cc_final: 0.8723 (Cg_endo) REVERT: D 93 ASN cc_start: 0.8766 (p0) cc_final: 0.8506 (p0) REVERT: I 3 GLN cc_start: 0.8477 (tt0) cc_final: 0.8206 (tp-100) REVERT: I 23 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8327 (mtpm) REVERT: I 43 GLN cc_start: 0.7654 (mt0) cc_final: 0.6932 (mp10) REVERT: L 2 ILE cc_start: 0.7514 (mt) cc_final: 0.7241 (mt) REVERT: L 17 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8272 (mp0) REVERT: L 54 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8382 (mtm-85) REVERT: L 81 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8582 (mt-10) REVERT: L 98 THR cc_start: 0.8795 (m) cc_final: 0.8209 (p) REVERT: A 23 LYS cc_start: 0.8443 (tttt) cc_final: 0.8186 (ttmt) outliers start: 20 outliers final: 4 residues processed: 251 average time/residue: 0.7440 time to fit residues: 206.4715 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 150 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 347 HIS E 465 ASN G 347 HIS H 465 ASN F 141 ASN B 6 GLN D 27 GLN I 31 ASN A 62 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.056210 restraints weight = 31951.961| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.47 r_work: 0.2584 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19146 Z= 0.225 Angle : 0.668 6.899 26166 Z= 0.342 Chirality : 0.045 0.178 3085 Planarity : 0.004 0.042 3191 Dihedral : 5.758 29.940 2464 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.63 % Favored : 97.20 % Rotamer: Outliers : 1.08 % Allowed : 8.25 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2246 helix: -0.25 (0.87), residues: 24 sheet: -0.17 (0.18), residues: 810 loop : 0.01 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.020 0.002 TYR G 121 PHE 0.019 0.002 PHE G 410 TRP 0.019 0.002 TRP H 178 HIS 0.009 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (19013) covalent geometry : angle 0.63826 / 0.34 (25809) SS BOND : bond 0.00398 / 0.21 ( 42) SS BOND : angle 0.87733 / 0.57 ( 84) hydrogen bonds : bond 0.04776 / 3.20 ( 592) hydrogen bonds : angle 7.10300 / 5.05 ( 1581) link_ALPHA1-2 : bond 0.00255 / 0.12 ( 4) link_ALPHA1-2 : angle 1.88553 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00304 / 0.19 ( 8) link_ALPHA1-3 : angle 1.68353 / 1.03 ( 24) link_ALPHA1-6 : bond 0.00231 / 0.13 ( 8) link_ALPHA1-6 : angle 1.52029 / 0.96 ( 24) link_BETA1-4 : bond 0.00436 / 0.26 ( 47) link_BETA1-4 : angle 1.82085 / 1.26 ( 141) link_NAG-ASN : bond 0.00418 / 0.25 ( 24) link_NAG-ASN : angle 2.53959 / 1.71 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9192 (tttt) cc_final: 0.8876 (ttpt) REVERT: G 150 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8283 (mtm180) REVERT: H 150 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7882 (mtp-110) REVERT: H 331 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 17 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 24 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7907 (ttm-80) REVERT: B 59 PRO cc_start: 0.9155 (Cg_exo) cc_final: 0.8906 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 81 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8564 (tm-30) REVERT: B 82 ASP cc_start: 0.9284 (m-30) cc_final: 0.8917 (m-30) REVERT: C 43 GLN cc_start: 0.8589 (mt0) cc_final: 0.8253 (mm-40) REVERT: C 45 LEU cc_start: 0.9203 (mt) cc_final: 0.9000 (mm) REVERT: C 89 GLU cc_start: 0.8942 (pm20) cc_final: 0.8670 (pm20) REVERT: C 98 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8052 (ttt-90) REVERT: D 59 PRO cc_start: 0.9147 (Cg_exo) cc_final: 0.8753 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7738 (ptm160) cc_final: 0.6488 (pmt170) REVERT: I 3 GLN cc_start: 0.8460 (tt0) cc_final: 0.8224 (tp-100) REVERT: I 43 GLN cc_start: 0.7737 (mt0) cc_final: 0.7040 (mp10) REVERT: L 54 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8339 (mtm-85) REVERT: L 81 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8506 (mp0) REVERT: L 82 ASP cc_start: 0.8986 (m-30) cc_final: 0.8733 (m-30) REVERT: L 92 ASN cc_start: 0.8814 (t0) cc_final: 0.8600 (t0) REVERT: L 98 THR cc_start: 0.8894 (m) cc_final: 0.8492 (p) REVERT: L 108 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8515 (ttpp) REVERT: A 23 LYS cc_start: 0.8461 (tttt) cc_final: 0.8191 (ttmt) REVERT: A 43 GLN cc_start: 0.8047 (mp10) cc_final: 0.7204 (mp10) outliers start: 21 outliers final: 6 residues processed: 240 average time/residue: 0.7250 time to fit residues: 191.9915 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 465 ASN B 27 GLN B 93 ASN A 32 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.057191 restraints weight = 31793.225| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.47 r_work: 0.2609 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19146 Z= 0.186 Angle : 0.628 6.528 26166 Z= 0.321 Chirality : 0.044 0.163 3085 Planarity : 0.004 0.047 3191 Dihedral : 5.533 28.148 2464 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 9.12 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2246 helix: -0.92 (0.82), residues: 28 sheet: -0.28 (0.17), residues: 835 loop : 0.06 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.018 0.002 TYR D 91 PHE 0.017 0.002 PHE G 410 TRP 0.017 0.001 TRP H 178 HIS 0.004 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (19013) covalent geometry : angle 0.60100 / 0.32 (25809) SS BOND : bond 0.00321 / 0.17 ( 42) SS BOND : angle 0.86904 / 0.56 ( 84) hydrogen bonds : bond 0.04277 / 2.85 ( 592) hydrogen bonds : angle 6.84902 / 4.86 ( 1581) link_ALPHA1-2 : bond 0.00340 / 0.16 ( 4) link_ALPHA1-2 : angle 1.76472 / 0.92 ( 12) link_ALPHA1-3 : bond 0.00357 / 0.21 ( 8) link_ALPHA1-3 : angle 1.56189 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00256 / 0.14 ( 8) link_ALPHA1-6 : angle 1.47949 / 0.93 ( 24) link_BETA1-4 : bond 0.00374 / 0.22 ( 47) link_BETA1-4 : angle 1.65393 / 1.13 ( 141) link_NAG-ASN : bond 0.00316 / 0.19 ( 24) link_NAG-ASN : angle 2.30934 / 1.56 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 ASP cc_start: 0.8727 (m-30) cc_final: 0.8343 (t70) REVERT: G 150 ARG cc_start: 0.8522 (mtt180) cc_final: 0.8280 (mtm180) REVERT: H 150 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7844 (mtp-110) REVERT: H 331 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8892 (p) REVERT: B 17 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 24 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7937 (ttm-80) REVERT: B 59 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8918 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 81 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8412 (tm-30) REVERT: B 82 ASP cc_start: 0.9252 (m-30) cc_final: 0.8933 (m-30) REVERT: B 104 LYS cc_start: 0.8995 (tppt) cc_final: 0.8767 (tppp) REVERT: C 43 GLN cc_start: 0.8650 (mt0) cc_final: 0.8328 (mm-40) REVERT: C 89 GLU cc_start: 0.8896 (pm20) cc_final: 0.8602 (pm20) REVERT: D 54 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8288 (mtm-85) REVERT: D 59 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8666 (Cg_endo) REVERT: D 109 ARG cc_start: 0.7667 (ptm160) cc_final: 0.6549 (pmt170) REVERT: I 3 GLN cc_start: 0.8439 (tt0) cc_final: 0.8232 (tp-100) REVERT: I 43 GLN cc_start: 0.7745 (mt0) cc_final: 0.7063 (mp10) REVERT: I 52 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8439 (mm) REVERT: L 17 GLU cc_start: 0.7349 (mp0) cc_final: 0.6811 (mp0) REVERT: L 54 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8340 (mtm-85) REVERT: L 81 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8510 (mp0) REVERT: L 82 ASP cc_start: 0.8891 (m-30) cc_final: 0.8653 (m-30) REVERT: L 92 ASN cc_start: 0.8828 (t0) cc_final: 0.8626 (t0) REVERT: L 98 THR cc_start: 0.8935 (m) cc_final: 0.8565 (p) REVERT: A 23 LYS cc_start: 0.8488 (tttt) cc_final: 0.8236 (ttmt) REVERT: A 43 GLN cc_start: 0.8050 (mp10) cc_final: 0.7251 (mp10) outliers start: 18 outliers final: 6 residues processed: 240 average time/residue: 0.7091 time to fit residues: 188.0316 Evaluate side-chains 228 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 156 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN F 141 ASN F 147 ASN B 93 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.055383 restraints weight = 31887.322| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.42 r_work: 0.2569 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19146 Z= 0.272 Angle : 0.662 7.095 26166 Z= 0.337 Chirality : 0.045 0.193 3085 Planarity : 0.004 0.041 3191 Dihedral : 5.596 28.236 2464 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.07 % Favored : 96.75 % Rotamer: Outliers : 1.19 % Allowed : 9.64 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2246 helix: -0.77 (0.84), residues: 28 sheet: -0.32 (0.17), residues: 847 loop : 0.01 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 87 TYR 0.020 0.002 TYR L 91 PHE 0.019 0.002 PHE G 410 TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 (19013) covalent geometry : angle 0.63285 / 0.33 (25809) SS BOND : bond 0.00446 / 0.24 ( 42) SS BOND : angle 0.88137 / 0.57 ( 84) hydrogen bonds : bond 0.04628 / 3.09 ( 592) hydrogen bonds : angle 6.89053 / 4.89 ( 1581) link_ALPHA1-2 : bond 0.00132 / 0.06 ( 4) link_ALPHA1-2 : angle 1.94860 / 1.01 ( 12) link_ALPHA1-3 : bond 0.00130 / 0.08 ( 8) link_ALPHA1-3 : angle 1.82260 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00105 / 0.05 ( 8) link_ALPHA1-6 : angle 1.61984 / 1.02 ( 24) link_BETA1-4 : bond 0.00376 / 0.23 ( 47) link_BETA1-4 : angle 1.68716 / 1.15 ( 141) link_NAG-ASN : bond 0.00526 / 0.32 ( 24) link_NAG-ASN : angle 2.54863 / 1.72 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 93 ASP cc_start: 0.8715 (m-30) cc_final: 0.8337 (t70) REVERT: G 150 ARG cc_start: 0.8550 (mtt180) cc_final: 0.8231 (mtm180) REVERT: H 150 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7773 (ttm110) REVERT: H 331 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8973 (p) REVERT: B 17 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 24 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7931 (ttm-80) REVERT: B 59 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8848 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 81 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8438 (tm-30) REVERT: B 82 ASP cc_start: 0.9207 (m-30) cc_final: 0.8819 (m-30) REVERT: C 43 GLN cc_start: 0.8646 (mt0) cc_final: 0.8302 (mm-40) REVERT: I 3 GLN cc_start: 0.8468 (tt0) cc_final: 0.8263 (tp-100) REVERT: I 23 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8310 (mtpm) REVERT: I 43 GLN cc_start: 0.7782 (mt0) cc_final: 0.7180 (mp10) REVERT: I 52 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8510 (mm) REVERT: L 17 GLU cc_start: 0.7392 (mp0) cc_final: 0.7028 (mp0) REVERT: L 54 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8389 (mtm-85) REVERT: L 81 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8516 (mp0) REVERT: L 98 THR cc_start: 0.8967 (m) cc_final: 0.8584 (p) REVERT: A 23 LYS cc_start: 0.8480 (tttt) cc_final: 0.8233 (ttmt) REVERT: A 43 GLN cc_start: 0.8097 (mp10) cc_final: 0.7280 (mp10) REVERT: A 73 ASP cc_start: 0.8290 (m-30) cc_final: 0.7672 (t0) outliers start: 23 outliers final: 5 residues processed: 233 average time/residue: 0.7771 time to fit residues: 199.6236 Evaluate side-chains 225 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN B 6 GLN B 93 ASN C 117 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.058456 restraints weight = 31544.171| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.45 r_work: 0.2639 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19146 Z= 0.142 Angle : 0.595 6.209 26166 Z= 0.305 Chirality : 0.043 0.159 3085 Planarity : 0.004 0.041 3191 Dihedral : 5.302 25.944 2464 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 0.72 % Allowed : 10.93 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2246 helix: -0.80 (0.82), residues: 28 sheet: -0.32 (0.17), residues: 855 loop : 0.17 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 100 TYR 0.017 0.002 TYR D 91 PHE 0.016 0.002 PHE F 410 TRP 0.017 0.001 TRP H 178 HIS 0.003 0.001 HIS H 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19013) covalent geometry : angle 0.57394 / 0.30 (25809) SS BOND : bond 0.00286 / 0.15 ( 42) SS BOND : angle 0.60858 / 0.40 ( 84) hydrogen bonds : bond 0.03895 / 2.59 ( 592) hydrogen bonds : angle 6.59922 / 4.68 ( 1581) link_ALPHA1-2 : bond 0.00431 / 0.20 ( 4) link_ALPHA1-2 : angle 1.65025 / 0.86 ( 12) link_ALPHA1-3 : bond 0.00450 / 0.26 ( 8) link_ALPHA1-3 : angle 1.45026 / 0.89 ( 24) link_ALPHA1-6 : bond 0.00326 / 0.18 ( 8) link_ALPHA1-6 : angle 1.44119 / 0.90 ( 24) link_BETA1-4 : bond 0.00376 / 0.22 ( 47) link_BETA1-4 : angle 1.45571 / 0.99 ( 141) link_NAG-ASN : bond 0.00231 / 0.14 ( 24) link_NAG-ASN : angle 2.07794 / 1.40 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 ASP cc_start: 0.8721 (m-30) cc_final: 0.8363 (t70) REVERT: G 150 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8243 (mtm180) REVERT: H 150 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7763 (ttm110) REVERT: B 17 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8277 (mm-30) REVERT: B 24 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7930 (ttm-80) REVERT: B 59 PRO cc_start: 0.9173 (Cg_exo) cc_final: 0.8913 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 81 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8407 (tm-30) REVERT: C 12 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8505 (mtpt) REVERT: C 43 GLN cc_start: 0.8625 (mt0) cc_final: 0.8268 (mm-40) REVERT: D 104 LYS cc_start: 0.8808 (tptm) cc_final: 0.8523 (tptp) REVERT: I 3 GLN cc_start: 0.8486 (tt0) cc_final: 0.8276 (tp-100) REVERT: I 23 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8208 (mtpm) REVERT: I 43 GLN cc_start: 0.7765 (mt0) cc_final: 0.7210 (mp10) REVERT: I 73 ASP cc_start: 0.8220 (m-30) cc_final: 0.7999 (t0) REVERT: I 117 ASN cc_start: 0.8423 (m110) cc_final: 0.8126 (m-40) REVERT: L 17 GLU cc_start: 0.7418 (mp0) cc_final: 0.6923 (mp0) REVERT: L 54 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8412 (mtm-85) REVERT: L 81 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8522 (mp0) REVERT: L 92 ASN cc_start: 0.8806 (t0) cc_final: 0.8576 (m-40) REVERT: L 98 THR cc_start: 0.8952 (m) cc_final: 0.8631 (p) REVERT: A 23 LYS cc_start: 0.8533 (tttt) cc_final: 0.8264 (ttmt) REVERT: A 43 GLN cc_start: 0.8223 (mp10) cc_final: 0.7434 (mp10) REVERT: A 73 ASP cc_start: 0.8348 (m-30) cc_final: 0.7733 (t70) REVERT: A 120 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8479 (pp30) outliers start: 14 outliers final: 4 residues processed: 239 average time/residue: 0.7619 time to fit residues: 201.0371 Evaluate side-chains 228 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 223 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain A residue 120 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 141 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN B 93 ASN A 117 ASN ** A 120 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 = 0.3232 r_free = 0.3232 target = 0.082334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.058945 restraints weight = 31883.379| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.47 r_work: 0.2650 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19146 Z= 0.142 Angle : 0.589 6.312 26166 Z= 0.301 Chirality : 0.043 0.162 3085 Planarity : 0.004 0.042 3191 Dihedral : 5.196 24.886 2464 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 1.03 % Allowed : 11.34 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2246 helix: -0.75 (0.82), residues: 28 sheet: -0.28 (0.17), residues: 855 loop : 0.19 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 100 TYR 0.021 0.002 TYR L 91 PHE 0.015 0.002 PHE F 410 TRP 0.015 0.001 TRP H 178 HIS 0.002 0.001 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (19013) covalent geometry : angle 0.56767 / 0.30 (25809) SS BOND : bond 0.00446 / 0.34 ( 42) SS BOND : angle 0.71937 / 0.48 ( 84) hydrogen bonds : bond 0.03821 / 2.53 ( 592) hydrogen bonds : angle 6.52097 / 4.63 ( 1581) link_ALPHA1-2 : bond 0.00415 / 0.19 ( 4) link_ALPHA1-2 : angle 1.67257 / 0.87 ( 12) link_ALPHA1-3 : bond 0.00427 / 0.25 ( 8) link_ALPHA1-3 : angle 1.48586 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00325 / 0.18 ( 8) link_ALPHA1-6 : angle 1.46294 / 0.92 ( 24) link_BETA1-4 : bond 0.00373 / 0.22 ( 47) link_BETA1-4 : angle 1.43209 / 0.97 ( 141) link_NAG-ASN : bond 0.00213 / 0.13 ( 24) link_NAG-ASN : angle 2.03878 / 1.38 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9232 (tttt) cc_final: 0.8891 (ttpt) REVERT: G 93 ASP cc_start: 0.8737 (m-30) cc_final: 0.8414 (t70) REVERT: G 150 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8222 (mtm180) REVERT: H 150 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7753 (ttm110) REVERT: B 17 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 24 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7907 (ttm-80) REVERT: B 59 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8927 (Cg_endo) REVERT: B 70 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 81 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8313 (tm-30) REVERT: B 104 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8777 (tppp) REVERT: C 12 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8529 (mtpt) REVERT: C 43 GLN cc_start: 0.8579 (mt0) cc_final: 0.8230 (mm-40) REVERT: C 87 ARG cc_start: 0.8244 (mpp80) cc_final: 0.8037 (mpp80) REVERT: C 117 ASN cc_start: 0.8310 (m110) cc_final: 0.7945 (p0) REVERT: D 17 GLU cc_start: 0.7649 (mp0) cc_final: 0.7367 (mp0) REVERT: D 61 ARG cc_start: 0.8893 (ptp90) cc_final: 0.8540 (ptp90) REVERT: I 23 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8228 (mtpm) REVERT: I 38 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7399 (ptt180) REVERT: I 43 GLN cc_start: 0.7749 (mt0) cc_final: 0.7232 (mp10) REVERT: I 52 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8410 (mm) REVERT: I 73 ASP cc_start: 0.8250 (m-30) cc_final: 0.8044 (t0) REVERT: I 117 ASN cc_start: 0.8391 (m110) cc_final: 0.8080 (m-40) REVERT: L 17 GLU cc_start: 0.7424 (mp0) cc_final: 0.7012 (mp0) REVERT: L 45 ARG cc_start: 0.8293 (ttt-90) cc_final: 0.7935 (ttt180) REVERT: L 54 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8417 (mtm-85) REVERT: L 81 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8534 (mp0) REVERT: L 92 ASN cc_start: 0.8826 (t0) cc_final: 0.8606 (m-40) REVERT: L 98 THR cc_start: 0.9020 (m) cc_final: 0.8683 (p) REVERT: A 23 LYS cc_start: 0.8531 (tttt) cc_final: 0.8273 (ttmt) REVERT: A 43 GLN cc_start: 0.8207 (mp10) cc_final: 0.7442 (mp10) REVERT: A 63 LYS cc_start: 0.9385 (mtpp) cc_final: 0.9083 (ptpp) REVERT: A 73 ASP cc_start: 0.8324 (m-30) cc_final: 0.7780 (t70) outliers start: 20 outliers final: 4 residues processed: 244 average time/residue: 0.7388 time to fit residues: 199.3470 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 226 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 192 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN F 141 ASN B 93 ASN I 3 GLN A 117 ASN A 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.055382 restraints weight = 31896.307| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.41 r_work: 0.2569 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 19146 Z= 0.304 Angle : 0.667 6.716 26166 Z= 0.340 Chirality : 0.046 0.180 3085 Planarity : 0.004 0.043 3191 Dihedral : 5.480 26.487 2464 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 0.98 % Allowed : 11.75 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2246 helix: -0.69 (0.85), residues: 28 sheet: -0.29 (0.17), residues: 847 loop : 0.06 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 100 TYR 0.028 0.002 TYR B 91 PHE 0.019 0.002 PHE G 410 TRP 0.016 0.002 TRP F 178 HIS 0.004 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (19013) covalent geometry : angle 0.63976 / 0.33 (25809) SS BOND : bond 0.00462 / 0.26 ( 42) SS BOND : angle 0.90086 / 0.58 ( 84) hydrogen bonds : bond 0.04639 / 3.08 ( 592) hydrogen bonds : angle 6.77141 / 4.82 ( 1581) link_ALPHA1-2 : bond 0.00135 / 0.06 ( 4) link_ALPHA1-2 : angle 1.94453 / 1.01 ( 12) link_ALPHA1-3 : bond 0.00109 / 0.07 ( 8) link_ALPHA1-3 : angle 1.90485 / 1.16 ( 24) link_ALPHA1-6 : bond 0.00093 / 0.05 ( 8) link_ALPHA1-6 : angle 1.65875 / 1.04 ( 24) link_BETA1-4 : bond 0.00365 / 0.23 ( 47) link_BETA1-4 : angle 1.58899 / 1.08 ( 141) link_NAG-ASN : bond 0.00601 / 0.37 ( 24) link_NAG-ASN : angle 2.51730 / 1.71 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9237 (tttt) cc_final: 0.8899 (ttpt) REVERT: G 93 ASP cc_start: 0.8724 (m-30) cc_final: 0.8406 (t70) REVERT: G 150 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8209 (mtm180) REVERT: H 150 ARG cc_start: 0.8003 (ttt180) cc_final: 0.7761 (ttm110) REVERT: H 331 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 17 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 24 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7911 (ttm-80) REVERT: B 70 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 81 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8285 (tm-30) REVERT: B 104 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (tppp) REVERT: C 12 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8443 (mtpt) REVERT: C 43 GLN cc_start: 0.8628 (mt0) cc_final: 0.8269 (mm-40) REVERT: C 87 ARG cc_start: 0.8313 (mpp80) cc_final: 0.8092 (mpp80) REVERT: C 117 ASN cc_start: 0.8327 (m110) cc_final: 0.7971 (p0) REVERT: D 17 GLU cc_start: 0.7730 (mp0) cc_final: 0.7439 (mp0) REVERT: D 61 ARG cc_start: 0.8880 (ptp90) cc_final: 0.8514 (ptp90) REVERT: I 23 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8166 (mtpm) REVERT: I 38 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7416 (ptt180) REVERT: I 43 GLN cc_start: 0.7798 (mt0) cc_final: 0.7263 (mp10) REVERT: I 52 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8473 (mm) REVERT: I 73 ASP cc_start: 0.8263 (m-30) cc_final: 0.8010 (t0) REVERT: I 117 ASN cc_start: 0.8459 (m110) cc_final: 0.8079 (m-40) REVERT: L 17 GLU cc_start: 0.7411 (mp0) cc_final: 0.6981 (mp0) REVERT: L 45 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8149 (ttt-90) REVERT: L 54 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8472 (mtm-85) REVERT: L 81 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8561 (mp0) REVERT: L 98 THR cc_start: 0.9039 (m) cc_final: 0.8698 (p) REVERT: A 13 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8345 (mmm160) REVERT: A 23 LYS cc_start: 0.8447 (tttt) cc_final: 0.8186 (ttmt) REVERT: A 63 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9110 (ptpp) outliers start: 19 outliers final: 5 residues processed: 231 average time/residue: 0.7465 time to fit residues: 189.8666 Evaluate side-chains 230 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 152 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN B 93 ASN A 117 ASN A 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.056596 restraints weight = 31828.526| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.45 r_work: 0.2596 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19146 Z= 0.223 Angle : 0.627 6.904 26166 Z= 0.321 Chirality : 0.044 0.170 3085 Planarity : 0.004 0.042 3191 Dihedral : 5.383 26.336 2464 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 0.88 % Allowed : 11.86 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2246 helix: -0.74 (0.85), residues: 28 sheet: -0.31 (0.17), residues: 855 loop : 0.13 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 100 TYR 0.023 0.002 TYR L 91 PHE 0.017 0.002 PHE G 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (19013) covalent geometry : angle 0.60353 / 0.32 (25809) SS BOND : bond 0.00364 / 0.20 ( 42) SS BOND : angle 0.76810 / 0.50 ( 84) hydrogen bonds : bond 0.04244 / 2.82 ( 592) hydrogen bonds : angle 6.65250 / 4.73 ( 1581) link_ALPHA1-2 : bond 0.00201 / 0.10 ( 4) link_ALPHA1-2 : angle 1.79704 / 0.93 ( 12) link_ALPHA1-3 : bond 0.00202 / 0.11 ( 8) link_ALPHA1-3 : angle 1.62430 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00182 / 0.09 ( 8) link_ALPHA1-6 : angle 1.54072 / 0.96 ( 24) link_BETA1-4 : bond 0.00338 / 0.20 ( 47) link_BETA1-4 : angle 1.44942 / 0.98 ( 141) link_NAG-ASN : bond 0.00401 / 0.24 ( 24) link_NAG-ASN : angle 2.25815 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9250 (tttt) cc_final: 0.8913 (ttpt) REVERT: G 93 ASP cc_start: 0.8704 (m-30) cc_final: 0.8423 (t70) REVERT: G 150 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8204 (mtm180) REVERT: H 150 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7762 (ttm110) REVERT: H 331 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.9026 (p) REVERT: B 17 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8287 (mm-30) REVERT: B 24 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7925 (ttm-80) REVERT: B 70 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 81 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8265 (tm-30) REVERT: B 104 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8754 (tppp) REVERT: C 10 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: C 12 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8476 (mtpt) REVERT: C 23 LYS cc_start: 0.8516 (mtpm) cc_final: 0.8276 (mmmt) REVERT: C 43 GLN cc_start: 0.8624 (mt0) cc_final: 0.8262 (mm-40) REVERT: C 87 ARG cc_start: 0.8315 (mpp80) cc_final: 0.8081 (mpp80) REVERT: C 98 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8213 (ttp-110) REVERT: C 117 ASN cc_start: 0.8340 (m110) cc_final: 0.7924 (p0) REVERT: D 17 GLU cc_start: 0.7751 (mp0) cc_final: 0.7432 (mp0) REVERT: D 33 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8308 (tm) REVERT: D 61 ARG cc_start: 0.8882 (ptp90) cc_final: 0.8540 (ptp90) REVERT: I 23 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8207 (mtpm) REVERT: I 38 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7390 (ptt180) REVERT: I 43 GLN cc_start: 0.7774 (mt0) cc_final: 0.7276 (mp10) REVERT: I 52 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8417 (mm) REVERT: I 73 ASP cc_start: 0.8259 (m-30) cc_final: 0.8013 (t0) REVERT: I 117 ASN cc_start: 0.8478 (m110) cc_final: 0.8100 (m-40) REVERT: L 17 GLU cc_start: 0.7418 (mp0) cc_final: 0.6988 (mp0) REVERT: L 45 ARG cc_start: 0.8357 (ttt-90) cc_final: 0.8012 (ttt180) REVERT: L 54 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8386 (mtm-85) REVERT: L 81 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8557 (mp0) REVERT: L 98 THR cc_start: 0.9053 (m) cc_final: 0.8668 (p) REVERT: A 23 LYS cc_start: 0.8458 (tttt) cc_final: 0.8192 (ttmt) REVERT: A 43 GLN cc_start: 0.8263 (mp10) cc_final: 0.7440 (mp10) REVERT: A 63 LYS cc_start: 0.9374 (mtpp) cc_final: 0.9124 (ptpp) REVERT: A 73 ASP cc_start: 0.8400 (m-30) cc_final: 0.7216 (p0) outliers start: 17 outliers final: 7 residues processed: 230 average time/residue: 0.7468 time to fit residues: 189.3038 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 120 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN H 465 ASN B 93 ASN I 3 GLN A 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.056818 restraints weight = 31669.275| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.45 r_work: 0.2603 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19146 Z= 0.204 Angle : 0.620 7.382 26166 Z= 0.317 Chirality : 0.044 0.169 3085 Planarity : 0.004 0.042 3191 Dihedral : 5.350 26.138 2464 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 11.91 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2246 helix: -0.79 (0.82), residues: 28 sheet: -0.30 (0.17), residues: 855 loop : 0.15 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 100 TYR 0.023 0.002 TYR L 91 PHE 0.017 0.002 PHE G 410 TRP 0.017 0.001 TRP H 178 HIS 0.003 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (19013) covalent geometry : angle 0.59726 / 0.31 (25809) SS BOND : bond 0.00334 / 0.19 ( 42) SS BOND : angle 0.72630 / 0.47 ( 84) hydrogen bonds : bond 0.04170 / 2.77 ( 592) hydrogen bonds : angle 6.64534 / 4.72 ( 1581) link_ALPHA1-2 : bond 0.00220 / 0.11 ( 4) link_ALPHA1-2 : angle 1.80702 / 0.93 ( 12) link_ALPHA1-3 : bond 0.00224 / 0.13 ( 8) link_ALPHA1-3 : angle 1.62649 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00208 / 0.12 ( 8) link_ALPHA1-6 : angle 1.54269 / 0.97 ( 24) link_BETA1-4 : bond 0.00333 / 0.20 ( 47) link_BETA1-4 : angle 1.43616 / 0.97 ( 141) link_NAG-ASN : bond 0.00374 / 0.23 ( 24) link_NAG-ASN : angle 2.23409 / 1.51 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4492 Ramachandran restraints generated. 2246 Oldfield, 0 Emsley, 2246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 LYS cc_start: 0.9243 (tttt) cc_final: 0.8903 (ttpt) REVERT: G 93 ASP cc_start: 0.8709 (m-30) cc_final: 0.8432 (t70) REVERT: G 150 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8229 (mtm180) REVERT: G 381 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8380 (mt-10) REVERT: H 150 ARG cc_start: 0.7997 (ttt180) cc_final: 0.7754 (ttm110) REVERT: H 331 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.9005 (p) REVERT: B 17 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 24 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7914 (ttm-80) REVERT: B 70 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 104 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8754 (tppp) REVERT: C 10 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: C 12 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8476 (mtpt) REVERT: C 23 LYS cc_start: 0.8556 (mtpm) cc_final: 0.8332 (mmmt) REVERT: C 43 GLN cc_start: 0.8633 (mt0) cc_final: 0.8262 (mm-40) REVERT: C 87 ARG cc_start: 0.8310 (mpp80) cc_final: 0.8074 (mpp80) REVERT: D 17 GLU cc_start: 0.7740 (mp0) cc_final: 0.7416 (mp0) REVERT: D 33 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8302 (tm) REVERT: D 61 ARG cc_start: 0.8867 (ptp90) cc_final: 0.8533 (ptp90) REVERT: I 23 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8222 (mtpm) REVERT: I 38 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7372 (ptt180) REVERT: I 43 GLN cc_start: 0.7742 (mt0) cc_final: 0.7209 (mp10) REVERT: I 52 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8417 (mm) REVERT: I 73 ASP cc_start: 0.8256 (m-30) cc_final: 0.7996 (t0) REVERT: L 17 GLU cc_start: 0.7419 (mp0) cc_final: 0.6987 (mp0) REVERT: L 45 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8013 (ttt180) REVERT: L 54 ARG cc_start: 0.8859 (mtm-85) cc_final: 0.8414 (mtm-85) REVERT: L 81 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8556 (mp0) REVERT: L 98 THR cc_start: 0.9045 (m) cc_final: 0.8698 (p) REVERT: A 13 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.7884 (mtp85) REVERT: A 23 LYS cc_start: 0.8455 (tttt) cc_final: 0.8186 (ttmt) REVERT: A 43 GLN cc_start: 0.8277 (mp10) cc_final: 0.7459 (mp10) REVERT: A 63 LYS cc_start: 0.9368 (mtpp) cc_final: 0.9125 (ptpp) REVERT: A 73 ASP cc_start: 0.8397 (m-30) cc_final: 0.7261 (p0) outliers start: 16 outliers final: 7 residues processed: 230 average time/residue: 0.7474 time to fit residues: 189.8043 Evaluate side-chains 234 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 331 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain A residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 121 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 465 ASN G 465 ASN H 465 ASN B 93 ASN I 3 GLN A 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.055439 restraints weight = 32061.063| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.42 r_work: 0.2573 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19146 Z= 0.289 Angle : 0.663 7.353 26166 Z= 0.339 Chirality : 0.046 0.176 3085 Planarity : 0.004 0.043 3191 Dihedral : 5.477 27.077 2464 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 0.88 % Allowed : 11.91 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.73 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2246 helix: -0.65 (0.83), residues: 28 sheet: -0.27 (0.17), residues: 847 loop : 0.06 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 100 TYR 0.025 0.002 TYR L 91 PHE 0.019 0.002 PHE G 410 TRP 0.016 0.002 TRP H 178 HIS 0.004 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.29 (19013) covalent geometry : angle 0.63838 / 0.33 (25809) SS BOND : bond 0.00443 / 0.25 ( 42) SS BOND : angle 0.82953 / 0.54 ( 84) hydrogen bonds : bond 0.04546 / 3.02 ( 592) hydrogen bonds : angle 6.75465 / 4.80 ( 1581) link_ALPHA1-2 : bond 0.00091 / 0.04 ( 4) link_ALPHA1-2 : angle 1.91932 / 1.00 ( 12) link_ALPHA1-3 : bond 0.00108 / 0.07 ( 8) link_ALPHA1-3 : angle 1.80979 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00107 / 0.06 ( 8) link_ALPHA1-6 : angle 1.63693 / 1.03 ( 24) link_BETA1-4 : bond 0.00349 / 0.22 ( 47) link_BETA1-4 : angle 1.51108 / 1.02 ( 141) link_NAG-ASN : bond 0.00574 / 0.35 ( 24) link_NAG-ASN : angle 2.44202 / 1.65 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8218.64 seconds wall clock time: 140 minutes 55.53 seconds (8455.53 seconds total)