Starting phenix.real_space_refine on Sat Aug 23 22:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3r_29709/08_2025/8g3r_29709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3r_29709/08_2025/8g3r_29709.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/8g3r_29709/08_2025/8g3r_29709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3r_29709/08_2025/8g3r_29709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3r_29709/08_2025/8g3r_29709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3r_29709/08_2025/8g3r_29709.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= 0.000 sd= 0.039 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 95 5.16 5 C 9192 2.51 5 N 2500 2.21 5 O 3107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14899 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "G" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} 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: "F" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3004 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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} Time building chain proxies: 3.75, per 1000 atoms: 0.25 Number of scatterers: 14899 At special positions: 0 Unit cell: (97.94, 119.52, 144.42, 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 95 16.00 O 3107 8.00 N 2500 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.08 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.00 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.06 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.10 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.11 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.08 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=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.09 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.09 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.09 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.08 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.09 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 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=2.02 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.05 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.08 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=2.02 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.07 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.10 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.12 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.09 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=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.04 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.09 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.04 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.10 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.09 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.08 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=2.13 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 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG d 1 " - " FUC d 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... 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 5 1 " - " ASN H 245 " " 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 e 1 " - " ASN E 245 " " 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 m 1 " - " ASN F 245 " " 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 u 1 " - " ASN G 245 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 445.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 30 sheets defined 3.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.539A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) 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 'G' and resid 247 through 251 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.903A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 104 through 110 removed outlier: 3.548A pdb=" N ALA F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 removed outlier: 3.535A pdb=" N ALA H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 146 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.724A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.888A 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: 4.697A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.952A 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: 4.108A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA E 201 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 216 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA E 203 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.523A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.477A 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: 5.405A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 353 through 356 removed outlier: 7.067A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.437A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.202A 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: 3.691A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.876A 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: 4.696A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.992A 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: 4.070A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA G 201 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL G 216 " --> pdb=" O ALA G 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 203 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER G 214 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE G 205 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.514A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.482A 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: 5.376A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.043A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.466A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.192A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.716A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.589A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.800A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 98 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.704A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.890A 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: 4.689A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.989A 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: 4.106A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 201 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 216 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA F 203 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER F 214 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE F 205 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.528A pdb=" N VAL F 231 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.474A 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: 5.413A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 356 removed outlier: 7.060A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.185A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, 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: 6.639A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA H 201 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL H 216 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA H 203 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 214 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE H 205 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 3.524A pdb=" N VAL H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.058A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.440A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.201A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1176 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: 2.64 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2915 1.32 - 1.45: 3943 1.45 - 1.58: 8234 1.58 - 1.71: 0 1.71 - 1.84: 114 Bond restraints: 15206 Sorted by residual: bond pdb=" N GLY H 286 " pdb=" CA GLY H 286 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.96e+01 bond pdb=" CA SER F 279 " pdb=" CB SER F 279 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N THR G 153 " pdb=" CA THR G 153 " ideal model delta sigma weight residual 1.455 1.492 -0.038 9.60e-03 1.09e+04 1.53e+01 bond pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.15e-02 7.56e+03 1.49e+01 bond pdb=" N THR H 153 " pdb=" CA THR H 153 " ideal model delta sigma weight residual 1.455 1.491 -0.037 9.60e-03 1.09e+04 1.46e+01 ... (remaining 15201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14645 1.66 - 3.32: 4884 3.32 - 4.98: 935 4.98 - 6.64: 157 6.64 - 8.30: 17 Bond angle restraints: 20638 Sorted by residual: angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" N ILE H 397 " pdb=" CA ILE H 397 " pdb=" C ILE H 397 " ideal model delta sigma weight residual 111.67 106.10 5.57 9.50e-01 1.11e+00 3.43e+01 angle pdb=" N ILE E 397 " pdb=" CA ILE E 397 " pdb=" C ILE E 397 " ideal model delta sigma weight residual 111.67 106.19 5.48 9.50e-01 1.11e+00 3.33e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.67 106.34 5.33 9.50e-01 1.11e+00 3.14e+01 angle pdb=" N ILE F 397 " pdb=" CA ILE F 397 " pdb=" C ILE F 397 " ideal model delta sigma weight residual 111.67 106.36 5.31 9.50e-01 1.11e+00 3.12e+01 ... (remaining 20633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.49: 9429 19.49 - 38.99: 512 38.99 - 58.48: 65 58.48 - 77.97: 48 77.97 - 97.46: 30 Dihedral angle restraints: 10084 sinusoidal: 5003 harmonic: 5081 Sorted by residual: dihedral pdb=" CA GLY G 297 " pdb=" C GLY G 297 " pdb=" N SER G 298 " pdb=" CA SER G 298 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLY E 297 " pdb=" C GLY E 297 " pdb=" N SER E 298 " pdb=" CA SER E 298 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY H 297 " pdb=" C GLY H 297 " pdb=" N SER H 298 " pdb=" CA SER H 298 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 10081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1701 0.095 - 0.190: 691 0.190 - 0.285: 88 0.285 - 0.380: 7 0.380 - 0.475: 4 Chirality restraints: 2491 Sorted by residual: 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 2.24 0.16 2.00e-02 2.50e+03 6.36e+01 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.66e+01 chirality pdb=" C1 FUC d 3 " pdb=" O6 NAG d 1 " pdb=" C2 FUC d 3 " pdb=" O5 FUC d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 2488 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.101 2.00e-02 2.50e+03 8.44e-02 8.91e+01 pdb=" C7 NAG i 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 1 " 0.077 2.00e-02 2.50e+03 6.44e-02 5.19e+01 pdb=" C7 NAG e 1 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG e 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG e 1 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG e 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " -0.067 2.00e-02 2.50e+03 5.65e-02 3.99e+01 pdb=" C7 NAG k 2 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " -0.056 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " 0.005 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 707 2.73 - 3.27: 14358 3.27 - 3.81: 25830 3.81 - 4.36: 36107 4.36 - 4.90: 55708 Nonbonded interactions: 132710 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E 501 " model vdw 2.187 2.510 nonbonded pdb=" O HIS F 347 " pdb="CA CA F2000 " model vdw 2.217 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.237 2.510 nonbonded pdb=" O HIS H 347 " pdb="CA CA H2000 " model vdw 2.280 2.510 nonbonded pdb=" O GLY F 345 " pdb="CA CA F2000 " model vdw 2.291 2.510 ... (remaining 132705 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 '5' selection = chain '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } 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: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.380 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 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 : 0.015 0.126 15325 Z= 0.989 Angle : 1.723 13.331 20957 Z= 1.076 Chirality : 0.094 0.475 2491 Planarity : 0.011 0.084 2549 Dihedral : 14.040 97.465 6732 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.80 (0.18), residues: 1778 helix: -0.48 (0.90), residues: 24 sheet: 0.26 (0.19), residues: 681 loop : -1.10 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG G 156 TYR 0.076 0.014 TYR H 423 PHE 0.051 0.012 PHE E 205 TRP 0.078 0.015 TRP G 115 HIS 0.033 0.007 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.01427 (15206) covalent geometry : angle 1.67132 (20638) SS BOND : bond 0.05832 ( 38) SS BOND : angle 2.39306 ( 76) hydrogen bonds : bond 0.16176 ( 436) hydrogen bonds : angle 8.86013 ( 1176) link_ALPHA1-2 : bond 0.00772 ( 4) link_ALPHA1-2 : angle 4.45343 ( 12) link_ALPHA1-3 : bond 0.01533 ( 8) link_ALPHA1-3 : angle 2.99109 ( 24) link_ALPHA1-6 : bond 0.00918 ( 8) link_ALPHA1-6 : angle 2.84999 ( 24) link_BETA1-4 : bond 0.01445 ( 32) link_BETA1-4 : angle 4.17135 ( 96) link_BETA1-6 : bond 0.02133 ( 1) link_BETA1-6 : angle 4.17517 ( 3) link_NAG-ASN : bond 0.01456 ( 28) link_NAG-ASN : angle 4.55228 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.423 Fit side-chains REVERT: E 150 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8352 (mtp85) REVERT: G 199 LYS cc_start: 0.8992 (tttt) cc_final: 0.8715 (tptt) REVERT: B 4 MET cc_start: 0.8921 (mmm) cc_final: 0.8023 (mmm) REVERT: B 24 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8214 (mtm110) REVERT: B 27 GLN cc_start: 0.8411 (mt0) cc_final: 0.8185 (mp10) REVERT: B 92 ASN cc_start: 0.9181 (t0) cc_final: 0.8925 (t0) REVERT: C 100 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8287 (tpp80) REVERT: C 116 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 125 THR cc_start: 0.8948 (m) cc_final: 0.8512 (p) REVERT: H 465 ASN cc_start: 0.9066 (m-40) cc_final: 0.8798 (m110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.6398 time to fit residues: 97.1313 Evaluate side-chains 101 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 HIS G 393 ASN C 117 ASN C 120 GLN F 465 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.067106 restraints weight = 22320.619| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.37 r_work: 0.2729 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15325 Z= 0.156 Angle : 0.706 8.304 20957 Z= 0.366 Chirality : 0.048 0.205 2491 Planarity : 0.004 0.034 2549 Dihedral : 9.151 74.126 3589 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.91 % Favored : 97.86 % Rotamer: Outliers : 0.90 % Allowed : 6.78 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.23 (0.19), residues: 1778 helix: -0.11 (0.92), residues: 24 sheet: 0.54 (0.19), residues: 656 loop : -0.58 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 403 TYR 0.023 0.002 TYR B 91 PHE 0.016 0.002 PHE E 132 TRP 0.023 0.002 TRP H 178 HIS 0.007 0.001 HIS E 336 Details of bonding type rmsd covalent geometry : bond 0.00328 (15206) covalent geometry : angle 0.67606 (20638) SS BOND : bond 0.00345 ( 38) SS BOND : angle 0.68756 ( 76) hydrogen bonds : bond 0.04734 ( 436) hydrogen bonds : angle 7.14481 ( 1176) link_ALPHA1-2 : bond 0.00328 ( 4) link_ALPHA1-2 : angle 1.65144 ( 12) link_ALPHA1-3 : bond 0.00962 ( 8) link_ALPHA1-3 : angle 2.16530 ( 24) link_ALPHA1-6 : bond 0.00550 ( 8) link_ALPHA1-6 : angle 1.23795 ( 24) link_BETA1-4 : bond 0.00435 ( 32) link_BETA1-4 : angle 1.71567 ( 96) link_BETA1-6 : bond 0.01014 ( 1) link_BETA1-6 : angle 1.77636 ( 3) link_NAG-ASN : bond 0.00212 ( 28) link_NAG-ASN : angle 2.45002 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7652 (mt-10) REVERT: G 83 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7594 (tp30) REVERT: G 199 LYS cc_start: 0.8444 (tttt) cc_final: 0.7974 (tptp) REVERT: B 27 GLN cc_start: 0.8052 (mt0) cc_final: 0.7622 (mp10) REVERT: B 70 GLU cc_start: 0.7474 (tp30) cc_final: 0.7162 (mm-30) REVERT: B 92 ASN cc_start: 0.8632 (t0) cc_final: 0.8278 (t0) REVERT: C 78 THR cc_start: 0.8135 (m) cc_final: 0.7543 (p) REVERT: C 98 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7528 (ttp80) REVERT: C 125 THR cc_start: 0.8907 (m) cc_final: 0.8663 (p) REVERT: F 199 LYS cc_start: 0.8279 (mttt) cc_final: 0.8042 (mttm) REVERT: H 221 GLU cc_start: 0.8157 (tt0) cc_final: 0.7908 (mt-10) REVERT: H 465 ASN cc_start: 0.8835 (m-40) cc_final: 0.8401 (m110) REVERT: H 467 MET cc_start: 0.7913 (ptm) cc_final: 0.7698 (ptm) outliers start: 14 outliers final: 6 residues processed: 127 average time/residue: 0.5790 time to fit residues: 80.3102 Evaluate side-chains 104 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain H residue 128 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 chunk 162 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066344 restraints weight = 22875.846| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.37 r_work: 0.2707 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15325 Z= 0.209 Angle : 0.688 7.025 20957 Z= 0.354 Chirality : 0.048 0.199 2491 Planarity : 0.004 0.039 2549 Dihedral : 8.576 68.533 3589 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.42 % Favored : 97.36 % Rotamer: Outliers : 1.55 % Allowed : 7.82 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.24 (0.19), residues: 1778 helix: -0.04 (0.93), residues: 24 sheet: 0.44 (0.19), residues: 679 loop : -0.54 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.020 0.002 TYR B 91 PHE 0.016 0.002 PHE E 410 TRP 0.020 0.002 TRP H 178 HIS 0.006 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00471 (15206) covalent geometry : angle 0.65532 (20638) SS BOND : bond 0.00310 ( 38) SS BOND : angle 1.06364 ( 76) hydrogen bonds : bond 0.04741 ( 436) hydrogen bonds : angle 6.88665 ( 1176) link_ALPHA1-2 : bond 0.00122 ( 4) link_ALPHA1-2 : angle 2.11966 ( 12) link_ALPHA1-3 : bond 0.00672 ( 8) link_ALPHA1-3 : angle 2.08930 ( 24) link_ALPHA1-6 : bond 0.00455 ( 8) link_ALPHA1-6 : angle 1.50622 ( 24) link_BETA1-4 : bond 0.00420 ( 32) link_BETA1-4 : angle 1.67307 ( 96) link_BETA1-6 : bond 0.01142 ( 1) link_BETA1-6 : angle 1.26519 ( 3) link_NAG-ASN : bond 0.00286 ( 28) link_NAG-ASN : angle 2.39964 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7761 (mt-10) REVERT: G 199 LYS cc_start: 0.8451 (tttt) cc_final: 0.8006 (tptp) REVERT: B 24 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7553 (mtp-110) REVERT: B 27 GLN cc_start: 0.8121 (mt0) cc_final: 0.7627 (mp10) REVERT: B 70 GLU cc_start: 0.7744 (tp30) cc_final: 0.7438 (tp30) REVERT: B 92 ASN cc_start: 0.8635 (t0) cc_final: 0.8236 (t0) REVERT: B 98 THR cc_start: 0.8894 (m) cc_final: 0.8352 (p) REVERT: C 23 LYS cc_start: 0.8396 (mttp) cc_final: 0.8183 (mtpm) REVERT: C 39 GLN cc_start: 0.7468 (tt0) cc_final: 0.7215 (tt0) REVERT: C 98 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7579 (ttp80) REVERT: C 117 ASN cc_start: 0.8550 (m-40) cc_final: 0.7972 (m110) REVERT: C 125 THR cc_start: 0.8932 (m) cc_final: 0.8672 (p) REVERT: F 199 LYS cc_start: 0.8406 (mttt) cc_final: 0.8185 (mttm) REVERT: H 221 GLU cc_start: 0.8267 (tt0) cc_final: 0.7984 (mt-10) REVERT: H 387 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8646 (mtpp) REVERT: H 400 ARG cc_start: 0.8139 (ptp-110) cc_final: 0.7687 (ptm160) REVERT: H 465 ASN cc_start: 0.8828 (m-40) cc_final: 0.8397 (m110) REVERT: H 467 MET cc_start: 0.7872 (ptm) cc_final: 0.7653 (ptm) outliers start: 24 outliers final: 8 residues processed: 128 average time/residue: 0.5503 time to fit residues: 77.6682 Evaluate side-chains 119 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 74 optimal weight: 0.6980 chunk 120 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069157 restraints weight = 22521.936| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.34 r_work: 0.2782 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15325 Z= 0.128 Angle : 0.611 8.613 20957 Z= 0.312 Chirality : 0.046 0.191 2491 Planarity : 0.003 0.041 2549 Dihedral : 7.559 56.633 3589 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.69 % Rotamer: Outliers : 1.16 % Allowed : 9.24 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.09 (0.19), residues: 1778 helix: 0.17 (0.96), residues: 24 sheet: 0.49 (0.19), residues: 670 loop : -0.39 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.017 0.001 TRP H 178 HIS 0.004 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00273 (15206) covalent geometry : angle 0.58598 (20638) SS BOND : bond 0.00217 ( 38) SS BOND : angle 0.95243 ( 76) hydrogen bonds : bond 0.03944 ( 436) hydrogen bonds : angle 6.48634 ( 1176) link_ALPHA1-2 : bond 0.00334 ( 4) link_ALPHA1-2 : angle 1.91538 ( 12) link_ALPHA1-3 : bond 0.00920 ( 8) link_ALPHA1-3 : angle 1.76989 ( 24) link_ALPHA1-6 : bond 0.00618 ( 8) link_ALPHA1-6 : angle 1.35983 ( 24) link_BETA1-4 : bond 0.00463 ( 32) link_BETA1-4 : angle 1.40375 ( 96) link_BETA1-6 : bond 0.00981 ( 1) link_BETA1-6 : angle 1.22897 ( 3) link_NAG-ASN : bond 0.00119 ( 28) link_NAG-ASN : angle 1.91892 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ASP cc_start: 0.8392 (p0) cc_final: 0.8162 (p0) REVERT: E 381 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 199 LYS cc_start: 0.8467 (tttt) cc_final: 0.8012 (tptp) REVERT: B 5 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 24 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7348 (mtp-110) REVERT: B 70 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: B 98 THR cc_start: 0.8913 (m) cc_final: 0.8449 (p) REVERT: C 11 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8518 (t) REVERT: C 23 LYS cc_start: 0.8441 (mttp) cc_final: 0.8186 (mtpm) REVERT: C 67 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7600 (ptm160) REVERT: C 78 THR cc_start: 0.8293 (m) cc_final: 0.7510 (p) REVERT: C 98 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7619 (ttp80) REVERT: C 117 ASN cc_start: 0.8443 (m-40) cc_final: 0.7904 (m110) REVERT: C 125 THR cc_start: 0.8948 (m) cc_final: 0.8581 (p) REVERT: H 221 GLU cc_start: 0.8229 (tt0) cc_final: 0.7939 (mt-10) REVERT: H 400 ARG cc_start: 0.8116 (ptp-110) cc_final: 0.7649 (ptm160) REVERT: H 465 ASN cc_start: 0.8810 (m-40) cc_final: 0.8413 (m110) outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.5402 time to fit residues: 76.7911 Evaluate side-chains 114 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.067685 restraints weight = 22682.070| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.36 r_work: 0.2753 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15325 Z= 0.174 Angle : 0.630 8.936 20957 Z= 0.321 Chirality : 0.047 0.223 2491 Planarity : 0.004 0.041 2549 Dihedral : 7.504 57.263 3589 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.41 % Rotamer: Outliers : 1.42 % Allowed : 9.69 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.12 (0.19), residues: 1778 helix: 0.35 (0.99), residues: 24 sheet: 0.43 (0.19), residues: 678 loop : -0.38 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.018 0.002 TYR B 91 PHE 0.015 0.002 PHE E 410 TRP 0.017 0.001 TRP H 178 HIS 0.004 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00390 (15206) covalent geometry : angle 0.60249 (20638) SS BOND : bond 0.00287 ( 38) SS BOND : angle 0.84061 ( 76) hydrogen bonds : bond 0.04156 ( 436) hydrogen bonds : angle 6.54621 ( 1176) link_ALPHA1-2 : bond 0.00181 ( 4) link_ALPHA1-2 : angle 2.01145 ( 12) link_ALPHA1-3 : bond 0.00708 ( 8) link_ALPHA1-3 : angle 1.98701 ( 24) link_ALPHA1-6 : bond 0.00504 ( 8) link_ALPHA1-6 : angle 1.47705 ( 24) link_BETA1-4 : bond 0.00385 ( 32) link_BETA1-4 : angle 1.50093 ( 96) link_BETA1-6 : bond 0.00916 ( 1) link_BETA1-6 : angle 1.22522 ( 3) link_NAG-ASN : bond 0.00231 ( 28) link_NAG-ASN : angle 2.07610 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7806 (mt-10) REVERT: G 199 LYS cc_start: 0.8443 (tttt) cc_final: 0.7998 (tptp) REVERT: G 344 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 5 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8305 (p) REVERT: B 24 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7285 (mtp-110) REVERT: B 70 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: B 92 ASN cc_start: 0.8572 (t0) cc_final: 0.8190 (t0) REVERT: B 98 THR cc_start: 0.8992 (m) cc_final: 0.8528 (p) REVERT: C 11 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 23 LYS cc_start: 0.8470 (mttp) cc_final: 0.8215 (mtpm) REVERT: C 67 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7448 (ptm160) REVERT: C 78 THR cc_start: 0.8305 (m) cc_final: 0.7593 (p) REVERT: C 98 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7656 (ttp80) REVERT: C 117 ASN cc_start: 0.8490 (m-40) cc_final: 0.7990 (m110) REVERT: C 125 THR cc_start: 0.8943 (m) cc_final: 0.8550 (p) REVERT: H 221 GLU cc_start: 0.8328 (tt0) cc_final: 0.8032 (mt-10) REVERT: H 387 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8700 (mtpp) REVERT: H 400 ARG cc_start: 0.8137 (ptp-110) cc_final: 0.7659 (ptm160) REVERT: H 465 ASN cc_start: 0.8816 (m-40) cc_final: 0.8444 (m110) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 0.5597 time to fit residues: 73.7490 Evaluate side-chains 117 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 0.0030 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.068084 restraints weight = 22707.525| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.36 r_work: 0.2745 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15325 Z= 0.156 Angle : 0.615 9.519 20957 Z= 0.312 Chirality : 0.046 0.210 2491 Planarity : 0.003 0.042 2549 Dihedral : 7.277 54.701 3589 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.08 % Favored : 97.69 % Rotamer: Outliers : 1.29 % Allowed : 10.21 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.11 (0.19), residues: 1778 helix: 0.48 (1.01), residues: 24 sheet: 0.41 (0.19), residues: 677 loop : -0.36 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00346 (15206) covalent geometry : angle 0.58990 (20638) SS BOND : bond 0.00224 ( 38) SS BOND : angle 0.76470 ( 76) hydrogen bonds : bond 0.03999 ( 436) hydrogen bonds : angle 6.45030 ( 1176) link_ALPHA1-2 : bond 0.00207 ( 4) link_ALPHA1-2 : angle 2.02052 ( 12) link_ALPHA1-3 : bond 0.00775 ( 8) link_ALPHA1-3 : angle 1.92406 ( 24) link_ALPHA1-6 : bond 0.00538 ( 8) link_ALPHA1-6 : angle 1.44864 ( 24) link_BETA1-4 : bond 0.00404 ( 32) link_BETA1-4 : angle 1.42967 ( 96) link_BETA1-6 : bond 0.00854 ( 1) link_BETA1-6 : angle 1.20313 ( 3) link_NAG-ASN : bond 0.00183 ( 28) link_NAG-ASN : angle 1.95700 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7830 (mt-10) REVERT: G 199 LYS cc_start: 0.8421 (tttt) cc_final: 0.8010 (tptp) REVERT: G 344 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 5 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8338 (p) REVERT: B 24 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7341 (mtp-110) REVERT: B 70 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: B 92 ASN cc_start: 0.8561 (t0) cc_final: 0.8184 (t0) REVERT: B 98 THR cc_start: 0.8994 (m) cc_final: 0.8573 (p) REVERT: C 11 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8504 (t) REVERT: C 23 LYS cc_start: 0.8489 (mttp) cc_final: 0.8235 (mtpm) REVERT: C 67 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7431 (ptm160) REVERT: C 78 THR cc_start: 0.8252 (m) cc_final: 0.7550 (p) REVERT: C 98 ARG cc_start: 0.8227 (ttp-110) cc_final: 0.7630 (ttp80) REVERT: C 117 ASN cc_start: 0.8436 (m-40) cc_final: 0.7750 (m110) REVERT: C 125 THR cc_start: 0.8948 (m) cc_final: 0.8544 (p) REVERT: H 221 GLU cc_start: 0.8323 (tt0) cc_final: 0.8023 (mt-10) REVERT: H 387 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8689 (mtpp) REVERT: H 400 ARG cc_start: 0.8166 (ptp-110) cc_final: 0.7687 (ptm160) REVERT: H 465 ASN cc_start: 0.8829 (m-40) cc_final: 0.8488 (m110) outliers start: 20 outliers final: 10 residues processed: 121 average time/residue: 0.5750 time to fit residues: 76.4227 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 153 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.068428 restraints weight = 22721.798| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.36 r_work: 0.2752 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15325 Z= 0.144 Angle : 0.608 9.587 20957 Z= 0.308 Chirality : 0.046 0.214 2491 Planarity : 0.003 0.042 2549 Dihedral : 7.106 52.540 3589 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 10.53 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.11 (0.19), residues: 1778 helix: 0.79 (1.06), residues: 24 sheet: 0.38 (0.19), residues: 677 loop : -0.34 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 152 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00316 (15206) covalent geometry : angle 0.58198 (20638) SS BOND : bond 0.00220 ( 38) SS BOND : angle 0.91955 ( 76) hydrogen bonds : bond 0.03895 ( 436) hydrogen bonds : angle 6.40724 ( 1176) link_ALPHA1-2 : bond 0.00224 ( 4) link_ALPHA1-2 : angle 1.99650 ( 12) link_ALPHA1-3 : bond 0.00805 ( 8) link_ALPHA1-3 : angle 1.88048 ( 24) link_ALPHA1-6 : bond 0.00556 ( 8) link_ALPHA1-6 : angle 1.45271 ( 24) link_BETA1-4 : bond 0.00407 ( 32) link_BETA1-4 : angle 1.39651 ( 96) link_BETA1-6 : bond 0.00869 ( 1) link_BETA1-6 : angle 1.22244 ( 3) link_NAG-ASN : bond 0.00161 ( 28) link_NAG-ASN : angle 1.91077 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 LYS cc_start: 0.8427 (tttt) cc_final: 0.8009 (tptt) REVERT: B 5 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 24 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7378 (mtp-110) REVERT: B 70 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: B 92 ASN cc_start: 0.8551 (t0) cc_final: 0.8168 (t0) REVERT: B 98 THR cc_start: 0.9022 (m) cc_final: 0.8604 (p) REVERT: C 11 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8501 (t) REVERT: C 23 LYS cc_start: 0.8497 (mttp) cc_final: 0.8245 (mtpm) REVERT: C 67 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7414 (ptm160) REVERT: C 78 THR cc_start: 0.8403 (m) cc_final: 0.7716 (p) REVERT: C 98 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7762 (ttp-110) REVERT: C 117 ASN cc_start: 0.8413 (m-40) cc_final: 0.7843 (m110) REVERT: C 125 THR cc_start: 0.8945 (m) cc_final: 0.8539 (p) REVERT: H 221 GLU cc_start: 0.8322 (tt0) cc_final: 0.8031 (mt-10) REVERT: H 387 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8683 (mtpp) REVERT: H 400 ARG cc_start: 0.8164 (ptp-110) cc_final: 0.7676 (ptm160) REVERT: H 465 ASN cc_start: 0.8815 (m-40) cc_final: 0.8482 (m110) outliers start: 19 outliers final: 9 residues processed: 116 average time/residue: 0.5948 time to fit residues: 75.6399 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067399 restraints weight = 22782.473| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.36 r_work: 0.2732 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15325 Z= 0.184 Angle : 0.629 9.541 20957 Z= 0.318 Chirality : 0.047 0.223 2491 Planarity : 0.004 0.043 2549 Dihedral : 7.223 54.194 3589 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.42 % Favored : 97.36 % Rotamer: Outliers : 1.23 % Allowed : 10.92 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.15 (0.19), residues: 1778 helix: 0.76 (1.10), residues: 24 sheet: 0.34 (0.19), residues: 677 loop : -0.37 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 24 TYR 0.018 0.002 TYR B 91 PHE 0.015 0.002 PHE E 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS E 336 Details of bonding type rmsd covalent geometry : bond 0.00412 (15206) covalent geometry : angle 0.60174 (20638) SS BOND : bond 0.00258 ( 38) SS BOND : angle 0.90800 ( 76) hydrogen bonds : bond 0.04099 ( 436) hydrogen bonds : angle 6.50528 ( 1176) link_ALPHA1-2 : bond 0.00124 ( 4) link_ALPHA1-2 : angle 2.08134 ( 12) link_ALPHA1-3 : bond 0.00686 ( 8) link_ALPHA1-3 : angle 2.03884 ( 24) link_ALPHA1-6 : bond 0.00465 ( 8) link_ALPHA1-6 : angle 1.50684 ( 24) link_BETA1-4 : bond 0.00368 ( 32) link_BETA1-4 : angle 1.46010 ( 96) link_BETA1-6 : bond 0.00853 ( 1) link_BETA1-6 : angle 1.21083 ( 3) link_NAG-ASN : bond 0.00268 ( 28) link_NAG-ASN : angle 2.00829 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7981 (ptp90) REVERT: G 199 LYS cc_start: 0.8427 (tttt) cc_final: 0.7994 (tptt) REVERT: G 344 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 4 MET cc_start: 0.8827 (mmm) cc_final: 0.8603 (mmm) REVERT: B 24 ARG cc_start: 0.7850 (mtp-110) cc_final: 0.7426 (mtp-110) REVERT: B 70 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: B 92 ASN cc_start: 0.8591 (t0) cc_final: 0.8200 (t0) REVERT: B 98 THR cc_start: 0.9005 (m) cc_final: 0.8592 (p) REVERT: C 23 LYS cc_start: 0.8516 (mttp) cc_final: 0.8260 (mtpm) REVERT: C 67 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7409 (ptm160) REVERT: C 78 THR cc_start: 0.8390 (m) cc_final: 0.7707 (p) REVERT: C 98 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7749 (ttp-110) REVERT: C 117 ASN cc_start: 0.8470 (m-40) cc_final: 0.8040 (m110) REVERT: C 125 THR cc_start: 0.8906 (m) cc_final: 0.8583 (p) REVERT: H 221 GLU cc_start: 0.8337 (tt0) cc_final: 0.8061 (mt-10) REVERT: H 387 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8512 (mtmm) REVERT: H 400 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7699 (ptm160) REVERT: H 465 ASN cc_start: 0.8829 (m-40) cc_final: 0.8501 (m110) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.5523 time to fit residues: 70.0059 Evaluate side-chains 114 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.067019 restraints weight = 22882.706| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.37 r_work: 0.2724 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15325 Z= 0.198 Angle : 0.638 9.987 20957 Z= 0.324 Chirality : 0.047 0.224 2491 Planarity : 0.004 0.043 2549 Dihedral : 7.318 55.430 3589 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.10 % Allowed : 10.98 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: -0.23 (0.19), residues: 1778 helix: 0.71 (1.09), residues: 24 sheet: 0.29 (0.19), residues: 685 loop : -0.42 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 152 TYR 0.018 0.002 TYR B 91 PHE 0.015 0.002 PHE E 410 TRP 0.016 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00444 (15206) covalent geometry : angle 0.61095 (20638) SS BOND : bond 0.00264 ( 38) SS BOND : angle 0.90726 ( 76) hydrogen bonds : bond 0.04179 ( 436) hydrogen bonds : angle 6.53247 ( 1176) link_ALPHA1-2 : bond 0.00099 ( 4) link_ALPHA1-2 : angle 2.10538 ( 12) link_ALPHA1-3 : bond 0.00651 ( 8) link_ALPHA1-3 : angle 2.08102 ( 24) link_ALPHA1-6 : bond 0.00440 ( 8) link_ALPHA1-6 : angle 1.51731 ( 24) link_BETA1-4 : bond 0.00362 ( 32) link_BETA1-4 : angle 1.48102 ( 96) link_BETA1-6 : bond 0.00846 ( 1) link_BETA1-6 : angle 1.20534 ( 3) link_NAG-ASN : bond 0.00291 ( 28) link_NAG-ASN : angle 2.02594 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7992 (ptp90) REVERT: G 199 LYS cc_start: 0.8424 (tttt) cc_final: 0.7989 (tptt) REVERT: G 344 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 4 MET cc_start: 0.8810 (mmm) cc_final: 0.8506 (mmm) REVERT: B 24 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7400 (mtp-110) REVERT: B 70 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: B 92 ASN cc_start: 0.8607 (t0) cc_final: 0.8218 (t0) REVERT: B 98 THR cc_start: 0.8982 (m) cc_final: 0.8566 (p) REVERT: C 23 LYS cc_start: 0.8520 (mttp) cc_final: 0.8277 (mtpm) REVERT: C 67 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7430 (ptm160) REVERT: C 98 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7546 (ttp80) REVERT: C 117 ASN cc_start: 0.8505 (m-40) cc_final: 0.7971 (m110) REVERT: C 125 THR cc_start: 0.8904 (m) cc_final: 0.8567 (p) REVERT: H 221 GLU cc_start: 0.8352 (tt0) cc_final: 0.8075 (mt-10) REVERT: H 387 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8475 (mtmm) REVERT: H 400 ARG cc_start: 0.8191 (ptp-110) cc_final: 0.7697 (ptm160) REVERT: H 465 ASN cc_start: 0.8825 (m-40) cc_final: 0.8495 (m110) outliers start: 17 outliers final: 10 residues processed: 112 average time/residue: 0.5722 time to fit residues: 70.3410 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8449 > 50: distance: 86 - 118: 32.877 distance: 89 - 115: 37.497 distance: 111 - 115: 34.035 distance: 115 - 116: 20.579 distance: 116 - 117: 44.501 distance: 116 - 119: 58.329 distance: 117 - 123: 69.634 distance: 119 - 120: 53.091 distance: 120 - 121: 31.206 distance: 120 - 122: 10.510 distance: 123 - 124: 39.822 distance: 124 - 127: 40.173 distance: 125 - 126: 39.692 distance: 127 - 128: 39.200 distance: 128 - 129: 40.489 distance: 129 - 130: 4.777 distance: 132 - 133: 47.123 distance: 133 - 136: 15.272 distance: 134 - 135: 25.074 distance: 134 - 140: 13.998 distance: 140 - 141: 32.403 distance: 141 - 142: 3.681 distance: 142 - 143: 38.097 distance: 142 - 144: 42.353 distance: 144 - 145: 19.165 distance: 145 - 146: 18.961 distance: 145 - 148: 5.330 distance: 146 - 147: 39.014 distance: 146 - 151: 57.128 distance: 148 - 149: 26.346 distance: 148 - 150: 25.110 distance: 151 - 152: 39.352 distance: 151 - 157: 11.408 distance: 152 - 153: 40.734 distance: 153 - 154: 38.783 distance: 153 - 158: 40.808 distance: 155 - 156: 49.005 distance: 156 - 157: 37.028 distance: 158 - 159: 40.426 distance: 159 - 162: 20.513 distance: 160 - 161: 39.048 distance: 160 - 169: 57.087 distance: 162 - 163: 44.602 distance: 163 - 165: 56.453 distance: 167 - 168: 56.287 distance: 169 - 170: 5.017 distance: 170 - 171: 40.188 distance: 170 - 173: 39.405 distance: 171 - 172: 39.846 distance: 171 - 179: 40.673 distance: 173 - 174: 3.674 distance: 174 - 175: 19.865 distance: 174 - 176: 48.677 distance: 175 - 177: 18.582 distance: 176 - 178: 27.527 distance: 180 - 181: 43.291 distance: 181 - 182: 44.630 distance: 181 - 187: 20.404 distance: 183 - 184: 66.600 distance: 184 - 185: 51.578 distance: 184 - 186: 41.599 distance: 189 - 190: 55.065 distance: 189 - 191: 34.773