Starting phenix.real_space_refine on Sat May 17 02:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3r_29709/05_2025/8g3r_29709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3r_29709/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3r_29709/05_2025/8g3r_29709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3r_29709/05_2025/8g3r_29709.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3r_29709/05_2025/8g3r_29709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3r_29709/05_2025/8g3r_29709.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.22, per 1000 atoms: 0.69 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: 5.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.64 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: 4.77 Time building geometry restraints manager: 5.87 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 469 or resid 501)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.290 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.078 0.015 TRP G 115 HIS 0.033 0.007 HIS E 347 PHE 0.051 0.012 PHE E 205 TYR 0.076 0.014 TYR H 423 ARG 0.024 0.003 ARG G 156 Details of bonding type rmsd link_NAG-ASN : bond 0.01456 ( 28) link_NAG-ASN : angle 4.55228 ( 84) 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_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) hydrogen bonds : bond 0.16176 ( 436) hydrogen bonds : angle 8.86013 ( 1176) link_BETA1-6 : bond 0.02133 ( 1) link_BETA1-6 : angle 4.17517 ( 3) SS BOND : bond 0.05832 ( 38) SS BOND : angle 2.39306 ( 76) covalent geometry : bond 0.01427 (15206) covalent geometry : angle 1.67132 (20638) *********************** 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 : 1.558 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: 1.4800 time to fit residues: 225.9790 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 : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.090956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.066965 restraints weight = 22503.638| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.38 r_work: 0.2726 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.025 15325 Z= 0.158 Angle : 0.708 7.559 20957 Z= 0.367 Chirality : 0.048 0.202 2491 Planarity : 0.004 0.034 2549 Dihedral : 9.152 74.196 3589 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.97 % Favored : 97.81 % Rotamer: Outliers : 0.90 % Allowed : 6.72 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1778 helix: -0.03 (0.93), residues: 24 sheet: 0.55 (0.19), residues: 656 loop : -0.58 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 178 HIS 0.008 0.001 HIS E 336 PHE 0.016 0.002 PHE E 132 TYR 0.023 0.002 TYR B 91 ARG 0.003 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 28) link_NAG-ASN : angle 2.49195 ( 84) link_ALPHA1-6 : bond 0.00524 ( 8) link_ALPHA1-6 : angle 1.23285 ( 24) link_BETA1-4 : bond 0.00443 ( 32) link_BETA1-4 : angle 1.74005 ( 96) link_ALPHA1-2 : bond 0.00312 ( 4) link_ALPHA1-2 : angle 1.70177 ( 12) link_ALPHA1-3 : bond 0.01016 ( 8) link_ALPHA1-3 : angle 2.21892 ( 24) hydrogen bonds : bond 0.04761 ( 436) hydrogen bonds : angle 7.14249 ( 1176) link_BETA1-6 : bond 0.00986 ( 1) link_BETA1-6 : angle 1.74479 ( 3) SS BOND : bond 0.00318 ( 38) SS BOND : angle 0.76614 ( 76) covalent geometry : bond 0.00332 (15206) covalent geometry : angle 0.67649 (20638) *********************** 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 133 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.760 Fit side-chains REVERT: E 381 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 83 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7580 (tp30) REVERT: G 199 LYS cc_start: 0.8447 (tttt) cc_final: 0.7977 (tptp) REVERT: B 24 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.7568 (mtp-110) REVERT: B 27 GLN cc_start: 0.8051 (mt0) cc_final: 0.7618 (mp10) REVERT: B 70 GLU cc_start: 0.7480 (tp30) cc_final: 0.7118 (mm-30) REVERT: B 92 ASN cc_start: 0.8635 (t0) cc_final: 0.8258 (t0) REVERT: C 78 THR cc_start: 0.8133 (m) cc_final: 0.7540 (p) REVERT: C 98 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7486 (ttp80) REVERT: C 117 ASN cc_start: 0.8497 (m-40) cc_final: 0.7725 (m110) REVERT: C 125 THR cc_start: 0.8908 (m) cc_final: 0.8661 (p) REVERT: F 199 LYS cc_start: 0.8282 (mttt) cc_final: 0.8047 (mttm) REVERT: H 221 GLU cc_start: 0.8162 (tt0) cc_final: 0.7908 (mt-10) REVERT: H 387 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (mtpp) REVERT: H 400 ARG cc_start: 0.8038 (ptp-110) cc_final: 0.7570 (ptm160) REVERT: H 465 ASN cc_start: 0.8838 (m-40) cc_final: 0.8411 (m110) REVERT: H 467 MET cc_start: 0.7916 (ptm) cc_final: 0.7698 (ptm) outliers start: 14 outliers final: 6 residues processed: 126 average time/residue: 1.3883 time to fit residues: 193.8488 Evaluate side-chains 104 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.065090 restraints weight = 22662.710| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.34 r_work: 0.2698 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15325 Z= 0.287 Angle : 0.736 7.472 20957 Z= 0.378 Chirality : 0.050 0.228 2491 Planarity : 0.004 0.039 2549 Dihedral : 8.856 71.006 3589 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.43 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1778 helix: -0.02 (0.98), residues: 24 sheet: 0.39 (0.19), residues: 679 loop : -0.64 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 178 HIS 0.007 0.002 HIS F 336 PHE 0.017 0.003 PHE E 410 TYR 0.022 0.002 TYR B 91 ARG 0.003 0.000 ARG E 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 28) link_NAG-ASN : angle 2.57181 ( 84) link_ALPHA1-6 : bond 0.00337 ( 8) link_ALPHA1-6 : angle 1.59013 ( 24) link_BETA1-4 : bond 0.00372 ( 32) link_BETA1-4 : angle 1.80954 ( 96) link_ALPHA1-2 : bond 0.00136 ( 4) link_ALPHA1-2 : angle 2.26699 ( 12) link_ALPHA1-3 : bond 0.00471 ( 8) link_ALPHA1-3 : angle 2.31068 ( 24) hydrogen bonds : bond 0.05088 ( 436) hydrogen bonds : angle 7.03117 ( 1176) link_BETA1-6 : bond 0.01154 ( 1) link_BETA1-6 : angle 1.29863 ( 3) SS BOND : bond 0.00444 ( 38) SS BOND : angle 1.27905 ( 76) covalent geometry : bond 0.00652 (15206) covalent geometry : angle 0.70004 (20638) *********************** 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 133 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7749 (mt-10) REVERT: G 199 LYS cc_start: 0.8432 (tttt) cc_final: 0.7972 (tptp) REVERT: B 24 ARG cc_start: 0.7939 (ttt-90) cc_final: 0.7475 (mtp-110) REVERT: B 27 GLN cc_start: 0.8103 (mt0) cc_final: 0.7601 (mp10) REVERT: B 70 GLU cc_start: 0.7819 (tp30) cc_final: 0.6982 (mm-30) REVERT: B 92 ASN cc_start: 0.8630 (t0) cc_final: 0.8222 (t0) REVERT: B 98 THR cc_start: 0.8927 (m) cc_final: 0.8434 (p) REVERT: C 23 LYS cc_start: 0.8411 (mttp) cc_final: 0.8199 (mtpm) REVERT: C 39 GLN cc_start: 0.7502 (tt0) cc_final: 0.7289 (tt0) REVERT: C 67 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7401 (ptm160) REVERT: C 98 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7578 (ttp80) REVERT: C 117 ASN cc_start: 0.8658 (m-40) cc_final: 0.7890 (m110) REVERT: C 125 THR cc_start: 0.8942 (m) cc_final: 0.8659 (p) REVERT: F 199 LYS cc_start: 0.8446 (mttt) cc_final: 0.8224 (mttm) REVERT: H 221 GLU cc_start: 0.8296 (tt0) cc_final: 0.8013 (mt-10) REVERT: H 387 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8662 (mtpp) REVERT: H 400 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7664 (ptm160) REVERT: H 465 ASN cc_start: 0.8832 (m-40) cc_final: 0.8410 (m110) REVERT: H 467 MET cc_start: 0.7958 (ptm) cc_final: 0.7681 (ptm) outliers start: 24 outliers final: 11 residues processed: 124 average time/residue: 1.3469 time to fit residues: 184.3477 Evaluate side-chains 120 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 67 SER Chi-restraints excluded: chain B residue 73 LEU 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 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 8 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067120 restraints weight = 22440.996| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.34 r_work: 0.2743 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15325 Z= 0.166 Angle : 0.648 8.575 20957 Z= 0.331 Chirality : 0.047 0.180 2491 Planarity : 0.003 0.040 2549 Dihedral : 8.112 62.793 3589 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.14 % Favored : 97.64 % Rotamer: Outliers : 1.16 % Allowed : 9.11 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1778 helix: 0.19 (1.00), residues: 24 sheet: 0.42 (0.19), residues: 668 loop : -0.58 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 178 HIS 0.004 0.001 HIS F 274 PHE 0.016 0.002 PHE E 410 TYR 0.019 0.002 TYR B 91 ARG 0.002 0.000 ARG G 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 28) link_NAG-ASN : angle 2.14895 ( 84) link_ALPHA1-6 : bond 0.00501 ( 8) link_ALPHA1-6 : angle 1.43226 ( 24) link_BETA1-4 : bond 0.00429 ( 32) link_BETA1-4 : angle 1.53189 ( 96) link_ALPHA1-2 : bond 0.00198 ( 4) link_ALPHA1-2 : angle 2.09062 ( 12) link_ALPHA1-3 : bond 0.00776 ( 8) link_ALPHA1-3 : angle 1.98916 ( 24) hydrogen bonds : bond 0.04277 ( 436) hydrogen bonds : angle 6.69724 ( 1176) link_BETA1-6 : bond 0.01178 ( 1) link_BETA1-6 : angle 1.28980 ( 3) SS BOND : bond 0.00354 ( 38) SS BOND : angle 1.06028 ( 76) covalent geometry : bond 0.00361 (15206) covalent geometry : angle 0.61830 (20638) *********************** 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 127 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7791 (mt-10) REVERT: G 199 LYS cc_start: 0.8468 (tttt) cc_final: 0.8008 (tptp) REVERT: G 344 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: B 24 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7580 (mtp-110) REVERT: B 70 GLU cc_start: 0.7824 (tp30) cc_final: 0.7392 (tp30) REVERT: B 92 ASN cc_start: 0.8569 (t0) cc_final: 0.8198 (t0) REVERT: B 98 THR cc_start: 0.8956 (m) cc_final: 0.8433 (p) REVERT: C 23 LYS cc_start: 0.8442 (mttp) cc_final: 0.8195 (mtpm) REVERT: C 39 GLN cc_start: 0.7539 (tt0) cc_final: 0.7299 (tt0) REVERT: C 67 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7498 (ptm160) REVERT: C 78 THR cc_start: 0.8361 (m) cc_final: 0.7564 (p) REVERT: C 98 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7588 (ttp80) REVERT: C 117 ASN cc_start: 0.8522 (m-40) cc_final: 0.7839 (m110) REVERT: C 125 THR cc_start: 0.8941 (m) cc_final: 0.8652 (p) REVERT: F 199 LYS cc_start: 0.8308 (mttt) cc_final: 0.8084 (mttm) REVERT: H 221 GLU cc_start: 0.8278 (tt0) cc_final: 0.7998 (mt-10) REVERT: H 387 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8654 (mtpp) REVERT: H 400 ARG cc_start: 0.8150 (ptp-110) cc_final: 0.7687 (ptm160) REVERT: H 465 ASN cc_start: 0.8827 (m-40) cc_final: 0.8427 (m110) outliers start: 18 outliers final: 9 residues processed: 119 average time/residue: 1.3240 time to fit residues: 173.9845 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 344 GLU 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 74 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 82 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066069 restraints weight = 22742.551| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.35 r_work: 0.2722 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15325 Z= 0.225 Angle : 0.673 8.886 20957 Z= 0.342 Chirality : 0.048 0.233 2491 Planarity : 0.004 0.041 2549 Dihedral : 8.057 63.539 3589 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.64 % Favored : 97.13 % Rotamer: Outliers : 1.36 % Allowed : 9.17 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1778 helix: 0.18 (1.03), residues: 24 sheet: 0.35 (0.19), residues: 668 loop : -0.58 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS F 274 PHE 0.017 0.002 PHE E 410 TYR 0.019 0.002 TYR B 91 ARG 0.004 0.000 ARG E 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 28) link_NAG-ASN : angle 2.25088 ( 84) link_ALPHA1-6 : bond 0.00399 ( 8) link_ALPHA1-6 : angle 1.53680 ( 24) link_BETA1-4 : bond 0.00362 ( 32) link_BETA1-4 : angle 1.62238 ( 96) link_ALPHA1-2 : bond 0.00093 ( 4) link_ALPHA1-2 : angle 2.17063 ( 12) link_ALPHA1-3 : bond 0.00578 ( 8) link_ALPHA1-3 : angle 2.17733 ( 24) hydrogen bonds : bond 0.04472 ( 436) hydrogen bonds : angle 6.72668 ( 1176) link_BETA1-6 : bond 0.00962 ( 1) link_BETA1-6 : angle 1.21532 ( 3) SS BOND : bond 0.00298 ( 38) SS BOND : angle 0.96018 ( 76) covalent geometry : bond 0.00509 (15206) covalent geometry : angle 0.64220 (20638) *********************** 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 128 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7808 (mt-10) REVERT: G 199 LYS cc_start: 0.8458 (tttt) cc_final: 0.7990 (tptp) REVERT: G 344 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 24 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7656 (mtp-110) REVERT: B 92 ASN cc_start: 0.8594 (t0) cc_final: 0.8224 (t0) REVERT: B 98 THR cc_start: 0.8997 (m) cc_final: 0.8504 (p) REVERT: C 23 LYS cc_start: 0.8465 (mttp) cc_final: 0.8215 (mtpm) REVERT: C 39 GLN cc_start: 0.7553 (tt0) cc_final: 0.7270 (tt0) REVERT: C 67 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7478 (ptm160) REVERT: C 78 THR cc_start: 0.8300 (m) cc_final: 0.7565 (p) REVERT: C 98 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7629 (ttp80) REVERT: C 117 ASN cc_start: 0.8541 (m-40) cc_final: 0.8034 (m110) REVERT: C 125 THR cc_start: 0.8944 (m) cc_final: 0.8633 (p) REVERT: F 199 LYS cc_start: 0.8410 (mttt) cc_final: 0.8185 (mttm) REVERT: H 221 GLU cc_start: 0.8310 (tt0) cc_final: 0.8055 (mt-10) REVERT: H 387 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (mtpp) REVERT: H 400 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7678 (ptm160) REVERT: H 465 ASN cc_start: 0.8835 (m-40) cc_final: 0.8453 (m110) outliers start: 21 outliers final: 11 residues processed: 118 average time/residue: 1.2913 time to fit residues: 168.5886 Evaluate side-chains 119 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 B residue 53 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 THR 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 128 LYS 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 78 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.066475 restraints weight = 22925.289| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.37 r_work: 0.2712 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2117 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= 0.198 Angle : 0.653 9.316 20957 Z= 0.331 Chirality : 0.047 0.197 2491 Planarity : 0.004 0.042 2549 Dihedral : 7.845 61.614 3589 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.31 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 9.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1778 helix: 0.29 (1.04), residues: 24 sheet: 0.33 (0.19), residues: 678 loop : -0.55 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS F 274 PHE 0.016 0.002 PHE E 410 TYR 0.018 0.002 TYR B 91 ARG 0.005 0.000 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 28) link_NAG-ASN : angle 2.12890 ( 84) link_ALPHA1-6 : bond 0.00431 ( 8) link_ALPHA1-6 : angle 1.50886 ( 24) link_BETA1-4 : bond 0.00377 ( 32) link_BETA1-4 : angle 1.55076 ( 96) link_ALPHA1-2 : bond 0.00113 ( 4) link_ALPHA1-2 : angle 2.13820 ( 12) link_ALPHA1-3 : bond 0.00652 ( 8) link_ALPHA1-3 : angle 2.10889 ( 24) hydrogen bonds : bond 0.04292 ( 436) hydrogen bonds : angle 6.64038 ( 1176) link_BETA1-6 : bond 0.00930 ( 1) link_BETA1-6 : angle 1.21523 ( 3) SS BOND : bond 0.00267 ( 38) SS BOND : angle 0.87602 ( 76) covalent geometry : bond 0.00444 (15206) covalent geometry : angle 0.62403 (20638) *********************** 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 128 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 199 LYS cc_start: 0.8446 (tttt) cc_final: 0.8009 (tptp) REVERT: G 344 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 24 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.7657 (mtp-110) REVERT: B 92 ASN cc_start: 0.8603 (t0) cc_final: 0.8238 (t0) REVERT: B 98 THR cc_start: 0.8993 (m) cc_final: 0.8541 (p) REVERT: C 23 LYS cc_start: 0.8481 (mttp) cc_final: 0.8233 (mtpm) REVERT: C 39 GLN cc_start: 0.7504 (tt0) cc_final: 0.7247 (tt0) REVERT: C 67 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7524 (ptm160) REVERT: C 78 THR cc_start: 0.8284 (m) cc_final: 0.7570 (p) REVERT: C 98 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7581 (ttp80) REVERT: C 117 ASN cc_start: 0.8500 (m-40) cc_final: 0.7959 (m110) REVERT: C 125 THR cc_start: 0.8935 (m) cc_final: 0.8602 (p) REVERT: F 199 LYS cc_start: 0.8367 (mttt) cc_final: 0.8159 (mttm) REVERT: H 221 GLU cc_start: 0.8328 (tt0) cc_final: 0.8053 (mt-10) REVERT: H 387 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8668 (mtpp) REVERT: H 400 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7710 (ptm160) REVERT: H 465 ASN cc_start: 0.8843 (m-40) cc_final: 0.8484 (m110) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 1.3389 time to fit residues: 180.9627 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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 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 128 LYS 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 142 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066217 restraints weight = 22938.607| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.37 r_work: 0.2709 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15325 Z= 0.209 Angle : 0.658 9.369 20957 Z= 0.333 Chirality : 0.047 0.204 2491 Planarity : 0.004 0.042 2549 Dihedral : 7.803 61.348 3589 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1778 helix: 0.32 (1.04), residues: 24 sheet: 0.31 (0.19), residues: 678 loop : -0.55 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS F 274 PHE 0.016 0.002 PHE E 410 TYR 0.018 0.002 TYR B 91 ARG 0.005 0.000 ARG E 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 28) link_NAG-ASN : angle 2.12887 ( 84) link_ALPHA1-6 : bond 0.00410 ( 8) link_ALPHA1-6 : angle 1.53091 ( 24) link_BETA1-4 : bond 0.00368 ( 32) link_BETA1-4 : angle 1.55527 ( 96) link_ALPHA1-2 : bond 0.00102 ( 4) link_ALPHA1-2 : angle 2.17283 ( 12) link_ALPHA1-3 : bond 0.00613 ( 8) link_ALPHA1-3 : angle 2.14216 ( 24) hydrogen bonds : bond 0.04306 ( 436) hydrogen bonds : angle 6.65256 ( 1176) link_BETA1-6 : bond 0.00918 ( 1) link_BETA1-6 : angle 1.21009 ( 3) SS BOND : bond 0.00373 ( 38) SS BOND : angle 1.04202 ( 76) covalent geometry : bond 0.00471 (15206) covalent geometry : angle 0.62839 (20638) *********************** 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 128 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 150 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: G 199 LYS cc_start: 0.8463 (tttt) cc_final: 0.8018 (tptp) REVERT: G 344 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 24 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7491 (mtp-110) REVERT: B 70 GLU cc_start: 0.7863 (tp30) cc_final: 0.7023 (mm-30) REVERT: B 92 ASN cc_start: 0.8610 (t0) cc_final: 0.8242 (t0) REVERT: B 98 THR cc_start: 0.8998 (m) cc_final: 0.8562 (p) REVERT: C 23 LYS cc_start: 0.8493 (mttp) cc_final: 0.8255 (mtpm) REVERT: C 39 GLN cc_start: 0.7510 (tt0) cc_final: 0.7286 (tt0) REVERT: C 67 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: C 98 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7568 (ttp80) REVERT: C 117 ASN cc_start: 0.8511 (m-40) cc_final: 0.7967 (m110) REVERT: C 125 THR cc_start: 0.8904 (m) cc_final: 0.8550 (p) REVERT: F 199 LYS cc_start: 0.8413 (mttt) cc_final: 0.8210 (mttm) REVERT: H 221 GLU cc_start: 0.8336 (tt0) cc_final: 0.8050 (mt-10) REVERT: H 387 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8665 (mtpp) REVERT: H 400 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7728 (ptm160) REVERT: H 465 ASN cc_start: 0.8840 (m-40) cc_final: 0.8482 (m110) outliers start: 22 outliers final: 16 residues processed: 119 average time/residue: 1.3288 time to fit residues: 174.9071 Evaluate side-chains 124 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 150 ARG 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 B residue 5 THR Chi-restraints excluded: chain B residue 34 VAL 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 C residue 67 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain H residue 128 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 170 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066065 restraints weight = 22830.003| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.36 r_work: 0.2706 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15325 Z= 0.220 Angle : 0.664 9.451 20957 Z= 0.336 Chirality : 0.048 0.207 2491 Planarity : 0.004 0.042 2549 Dihedral : 7.816 61.506 3589 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.36 % Allowed : 10.08 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1778 helix: 0.26 (1.03), residues: 24 sheet: 0.29 (0.19), residues: 677 loop : -0.56 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS F 274 PHE 0.016 0.002 PHE E 410 TYR 0.019 0.002 TYR B 91 ARG 0.002 0.000 ARG C 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 28) link_NAG-ASN : angle 2.13190 ( 84) link_ALPHA1-6 : bond 0.00381 ( 8) link_ALPHA1-6 : angle 1.55248 ( 24) link_BETA1-4 : bond 0.00358 ( 32) link_BETA1-4 : angle 1.56284 ( 96) link_ALPHA1-2 : bond 0.00086 ( 4) link_ALPHA1-2 : angle 2.20176 ( 12) link_ALPHA1-3 : bond 0.00588 ( 8) link_ALPHA1-3 : angle 2.18642 ( 24) hydrogen bonds : bond 0.04358 ( 436) hydrogen bonds : angle 6.67655 ( 1176) link_BETA1-6 : bond 0.00898 ( 1) link_BETA1-6 : angle 1.20675 ( 3) SS BOND : bond 0.00354 ( 38) SS BOND : angle 0.99252 ( 76) covalent geometry : bond 0.00497 (15206) covalent geometry : angle 0.63519 (20638) *********************** 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 127 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 LYS cc_start: 0.8448 (tttt) cc_final: 0.8010 (tptp) REVERT: G 344 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 24 ARG cc_start: 0.7925 (ttt-90) cc_final: 0.7575 (mtp-110) REVERT: B 70 GLU cc_start: 0.7927 (tp30) cc_final: 0.7434 (tp30) REVERT: B 92 ASN cc_start: 0.8613 (t0) cc_final: 0.8239 (t0) REVERT: B 98 THR cc_start: 0.9006 (m) cc_final: 0.8574 (p) REVERT: C 23 LYS cc_start: 0.8474 (mttp) cc_final: 0.8225 (mtpm) REVERT: C 39 GLN cc_start: 0.7582 (tt0) cc_final: 0.7333 (tt0) REVERT: C 67 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: C 78 THR cc_start: 0.8419 (m) cc_final: 0.7672 (p) REVERT: C 98 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7490 (ttp80) REVERT: C 117 ASN cc_start: 0.8532 (m-40) cc_final: 0.7983 (m110) REVERT: C 125 THR cc_start: 0.8902 (m) cc_final: 0.8544 (p) REVERT: F 199 LYS cc_start: 0.8377 (mttt) cc_final: 0.8164 (mttm) REVERT: H 221 GLU cc_start: 0.8372 (tt0) cc_final: 0.8094 (mt-10) REVERT: H 387 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8654 (mtpp) REVERT: H 400 ARG cc_start: 0.8191 (ptp-110) cc_final: 0.7718 (ptm160) REVERT: H 465 ASN cc_start: 0.8844 (m-40) cc_final: 0.8504 (m110) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 1.2754 time to fit residues: 169.5124 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 B residue 5 THR Chi-restraints excluded: chain B residue 53 THR 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 157 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain H residue 128 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 164 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 0.0370 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.066768 restraints weight = 22730.173| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.37 r_work: 0.2731 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15325 Z= 0.155 Angle : 0.627 9.880 20957 Z= 0.317 Chirality : 0.046 0.210 2491 Planarity : 0.003 0.042 2549 Dihedral : 7.459 56.992 3589 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.24 % Rotamer: Outliers : 1.16 % Allowed : 10.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1778 helix: 0.46 (1.04), residues: 24 sheet: 0.30 (0.19), residues: 677 loop : -0.49 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 PHE 0.015 0.002 PHE E 410 TYR 0.016 0.002 TYR B 91 ARG 0.004 0.000 ARG E 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 28) link_NAG-ASN : angle 1.94250 ( 84) link_ALPHA1-6 : bond 0.00502 ( 8) link_ALPHA1-6 : angle 1.48093 ( 24) link_BETA1-4 : bond 0.00406 ( 32) link_BETA1-4 : angle 1.42934 ( 96) link_ALPHA1-2 : bond 0.00186 ( 4) link_ALPHA1-2 : angle 2.10674 ( 12) link_ALPHA1-3 : bond 0.00780 ( 8) link_ALPHA1-3 : angle 1.97185 ( 24) hydrogen bonds : bond 0.04004 ( 436) hydrogen bonds : angle 6.52010 ( 1176) link_BETA1-6 : bond 0.00873 ( 1) link_BETA1-6 : angle 1.22209 ( 3) SS BOND : bond 0.00257 ( 38) SS BOND : angle 0.88537 ( 76) covalent geometry : bond 0.00341 (15206) covalent geometry : angle 0.60165 (20638) *********************** 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 128 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 LYS cc_start: 0.8451 (tttt) cc_final: 0.8015 (tptp) REVERT: G 344 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: B 24 ARG cc_start: 0.7844 (ttt-90) cc_final: 0.7491 (mtp-110) REVERT: B 70 GLU cc_start: 0.7892 (tp30) cc_final: 0.7396 (tp30) REVERT: B 73 LEU cc_start: 0.8823 (tt) cc_final: 0.8615 (tm) REVERT: B 92 ASN cc_start: 0.8587 (t0) cc_final: 0.8203 (t0) REVERT: B 98 THR cc_start: 0.8989 (m) cc_final: 0.8560 (p) REVERT: C 23 LYS cc_start: 0.8474 (mttp) cc_final: 0.8226 (mtpm) REVERT: C 39 GLN cc_start: 0.7516 (tt0) cc_final: 0.7248 (tt0) REVERT: C 67 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7520 (ptm160) REVERT: C 78 THR cc_start: 0.8390 (m) cc_final: 0.7666 (p) REVERT: C 98 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7497 (ttp80) REVERT: C 117 ASN cc_start: 0.8479 (m-40) cc_final: 0.7943 (m110) REVERT: C 125 THR cc_start: 0.8892 (m) cc_final: 0.8532 (p) REVERT: F 199 LYS cc_start: 0.8350 (mttt) cc_final: 0.8141 (mttm) REVERT: H 221 GLU cc_start: 0.8339 (tt0) cc_final: 0.8053 (mt-10) REVERT: H 387 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8472 (mtmm) REVERT: H 400 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7711 (ptm160) REVERT: H 465 ASN cc_start: 0.8834 (m-40) cc_final: 0.8494 (m110) outliers start: 18 outliers final: 13 residues processed: 121 average time/residue: 1.3753 time to fit residues: 183.3987 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ARG 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 F residue 238 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain H residue 128 LYS 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 ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 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 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 = 0.3287 r_free = 0.3287 target = 0.091578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.068078 restraints weight = 22689.716| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.37 r_work: 0.2757 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15325 Z= 0.134 Angle : 0.602 9.930 20957 Z= 0.304 Chirality : 0.046 0.215 2491 Planarity : 0.003 0.043 2549 Dihedral : 6.999 50.588 3589 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.64 % Favored : 97.13 % Rotamer: Outliers : 1.03 % Allowed : 10.53 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1778 helix: 0.63 (1.04), residues: 24 sheet: 0.34 (0.19), residues: 679 loop : -0.42 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 PHE 0.013 0.002 PHE E 410 TYR 0.016 0.002 TYR B 91 ARG 0.002 0.000 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 28) link_NAG-ASN : angle 1.81146 ( 84) link_ALPHA1-6 : bond 0.00583 ( 8) link_ALPHA1-6 : angle 1.44367 ( 24) link_BETA1-4 : bond 0.00421 ( 32) link_BETA1-4 : angle 1.34557 ( 96) link_ALPHA1-2 : bond 0.00240 ( 4) link_ALPHA1-2 : angle 1.98737 ( 12) link_ALPHA1-3 : bond 0.00855 ( 8) link_ALPHA1-3 : angle 1.81366 ( 24) hydrogen bonds : bond 0.03769 ( 436) hydrogen bonds : angle 6.37390 ( 1176) link_BETA1-6 : bond 0.00815 ( 1) link_BETA1-6 : angle 1.22485 ( 3) SS BOND : bond 0.00240 ( 38) SS BOND : angle 0.79359 ( 76) covalent geometry : bond 0.00292 (15206) covalent geometry : angle 0.57910 (20638) ********************** REFINEMENT MACRO_CYCLE 10 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 125 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8271 (pttm) REVERT: E 150 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7956 (mtp180) REVERT: E 151 ASP cc_start: 0.7376 (p0) cc_final: 0.6671 (t0) REVERT: G 199 LYS cc_start: 0.8425 (tttt) cc_final: 0.8001 (tptp) REVERT: B 5 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 24 ARG cc_start: 0.7831 (ttt-90) cc_final: 0.7409 (mtp-110) REVERT: B 70 GLU cc_start: 0.7938 (tp30) cc_final: 0.7429 (tp30) REVERT: B 73 LEU cc_start: 0.8789 (tt) cc_final: 0.8553 (tm) REVERT: B 92 ASN cc_start: 0.8525 (t0) cc_final: 0.8152 (t0) REVERT: B 98 THR cc_start: 0.8979 (m) cc_final: 0.8545 (p) REVERT: C 23 LYS cc_start: 0.8470 (mttp) cc_final: 0.8221 (mtpm) REVERT: C 67 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7271 (ptm160) REVERT: C 78 THR cc_start: 0.8438 (m) cc_final: 0.7702 (p) REVERT: C 98 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7481 (ttp80) REVERT: C 117 ASN cc_start: 0.8446 (m-40) cc_final: 0.7941 (m110) REVERT: C 125 THR cc_start: 0.8879 (m) cc_final: 0.8514 (p) REVERT: H 221 GLU cc_start: 0.8301 (tt0) cc_final: 0.8019 (mt-10) REVERT: H 387 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: H 400 ARG cc_start: 0.8167 (ptp-110) cc_final: 0.7691 (ptm160) REVERT: H 465 ASN cc_start: 0.8799 (m-40) cc_final: 0.8466 (m110) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 1.2895 time to fit residues: 173.0562 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ARG 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 F residue 238 THR 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 ************** Weight determination summary: number of chunks: 174 random chunks: chunk 37 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 144 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 155 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.092909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.069488 restraints weight = 22557.415| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.35 r_work: 0.2775 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15325 Z= 0.119 Angle : 0.586 9.665 20957 Z= 0.296 Chirality : 0.045 0.215 2491 Planarity : 0.003 0.042 2549 Dihedral : 6.703 49.552 3589 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.24 % Rotamer: Outliers : 0.84 % Allowed : 11.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1778 helix: 0.99 (1.09), residues: 24 sheet: 0.29 (0.19), residues: 699 loop : -0.28 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS F 274 PHE 0.013 0.002 PHE G 410 TYR 0.015 0.001 TYR B 91 ARG 0.002 0.000 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 28) link_NAG-ASN : angle 1.73977 ( 84) link_ALPHA1-6 : bond 0.00627 ( 8) link_ALPHA1-6 : angle 1.42900 ( 24) link_BETA1-4 : bond 0.00424 ( 32) link_BETA1-4 : angle 1.29118 ( 96) link_ALPHA1-2 : bond 0.00279 ( 4) link_ALPHA1-2 : angle 1.92938 ( 12) link_ALPHA1-3 : bond 0.00891 ( 8) link_ALPHA1-3 : angle 1.73584 ( 24) hydrogen bonds : bond 0.03649 ( 436) hydrogen bonds : angle 6.26157 ( 1176) link_BETA1-6 : bond 0.00783 ( 1) link_BETA1-6 : angle 1.23060 ( 3) SS BOND : bond 0.00214 ( 38) SS BOND : angle 0.75186 ( 76) covalent geometry : bond 0.00256 (15206) covalent geometry : angle 0.56460 (20638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10372.50 seconds wall clock time: 179 minutes 55.31 seconds (10795.31 seconds total)