Starting phenix.real_space_refine on Fri Jul 3 16:53:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3r_29709/07_2026/8g3r_29709.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 C 9192 2.51 5 N 2500 2.21 5 O 3107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 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 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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: 2.73, per 1000 atoms: 0.18 Number of scatterers: 14899 At special positions: 0 Unit cell: (97.94, 119.52, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 95 16.00 O 3107 8.00 N 2500 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.08 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.00 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.06 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.10 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.11 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.08 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.07 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.16 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.09 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.09 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.09 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.08 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.09 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 417 " distance=2.05 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.08 Simple disulfide: pdb=" SG CYS F 175 " - pdb=" SG CYS F 193 " distance=2.02 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 230 " distance=2.07 Simple disulfide: pdb=" SG CYS F 232 " - pdb=" SG CYS F 237 " distance=2.10 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 291 " distance=2.12 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 289 " distance=2.09 Simple disulfide: pdb=" SG CYS F 318 " - pdb=" SG CYS F 337 " distance=2.08 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.04 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.09 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.04 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.07 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.10 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.09 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.08 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG d 1 " - " FUC d 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG 1 1 " - " ASN H 86 " " NAG 2 1 " - " ASN H 146 " " NAG 3 1 " - " ASN H 200 " " NAG 4 1 " - " ASN H 234 " " NAG 5 1 " - " ASN H 245 " " NAG 6 1 " - " ASN H 329 " " NAG 7 1 " - " ASN H 367 " " NAG a 1 " - " ASN E 86 " " NAG b 1 " - " ASN E 146 " " NAG c 1 " - " ASN E 200 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 245 " " NAG f 1 " - " ASN E 329 " " NAG g 1 " - " ASN E 367 " " NAG i 1 " - " ASN F 86 " " NAG j 1 " - " ASN F 146 " " NAG k 1 " - " ASN F 200 " " NAG l 1 " - " ASN F 234 " " NAG m 1 " - " ASN F 245 " " NAG n 1 " - " ASN F 329 " " NAG o 1 " - " ASN F 367 " " NAG q 1 " - " ASN G 86 " " NAG r 1 " - " ASN G 146 " " NAG s 1 " - " ASN G 200 " " NAG t 1 " - " ASN G 234 " " NAG u 1 " - " ASN G 245 " " NAG v 1 " - " ASN G 329 " " NAG w 1 " - " ASN G 367 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 480.9 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 30 sheets defined 3.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.539A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.903A pdb=" N PHE B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 104 through 110 removed outlier: 3.548A pdb=" N ALA F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'H' and resid 104 through 110 removed outlier: 3.535A pdb=" N ALA H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 146 Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.724A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.697A pdb=" N TRP E 115 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR E 138 " --> pdb=" O TRP E 115 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN E 136 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU E 158 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS E 172 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 179 through 184 removed outlier: 4.108A pdb=" N ASP E 197 " --> pdb=" O ASN E 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA E 201 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 216 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA E 203 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 214 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE E 205 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 233 removed outlier: 6.523A pdb=" N GLU E 258 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU E 277 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG E 292 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 353 through 356 removed outlier: 7.067A pdb=" N ASN E 402 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N GLU E 375 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ARG E 400 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE E 377 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 13.437A pdb=" N VAL E 398 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N VAL E 379 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 16.202A pdb=" N VAL E 396 " --> pdb=" O VAL E 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 96 through 102 removed outlier: 3.691A pdb=" N GLY G 96 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 445 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS G 102 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE G 443 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.696A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.070A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA G 201 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL G 216 " --> pdb=" O ALA G 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 203 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER G 214 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE G 205 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.514A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.376A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 353 through 356 removed outlier: 7.043A pdb=" N ASN G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.449A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.466A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.192A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.716A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.589A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.240A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.800A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG C 98 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'F' and resid 96 through 102 removed outlier: 3.704A pdb=" N GLY F 96 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL F 445 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS F 102 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE F 443 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ARG F 420 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 124 removed outlier: 4.689A pdb=" N TRP F 115 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR F 138 " --> pdb=" O TRP F 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR F 117 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN F 136 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU F 119 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU F 134 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 157 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 158 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS F 172 " --> pdb=" O MET F 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 184 removed outlier: 4.106A pdb=" N ASP F 197 " --> pdb=" O ASN F 200 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 201 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL F 216 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA F 203 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER F 214 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE F 205 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.528A pdb=" N VAL F 231 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU F 258 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 283 removed outlier: 5.413A pdb=" N GLU F 277 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG F 292 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 356 removed outlier: 7.060A pdb=" N ASN F 402 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLU F 375 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N ARG F 400 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N PHE F 377 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 13.405A pdb=" N VAL F 398 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 15.427A pdb=" N VAL F 379 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 16.185A pdb=" N VAL F 396 " --> pdb=" O VAL F 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.696A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.704A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA H 201 " --> pdb=" O VAL H 216 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL H 216 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA H 203 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 214 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE H 205 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 3.524A pdb=" N VAL H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.403A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 353 through 356 removed outlier: 7.058A pdb=" N ASN H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.440A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.201A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.56 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 - 17.99: 7778 17.99 - 35.98: 526 35.98 - 53.97: 90 53.97 - 71.96: 21 71.96 - 89.95: 20 Dihedral angle restraints: 8435 sinusoidal: 3354 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 8432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1701 0.095 - 0.190: 691 0.190 - 0.285: 88 0.285 - 0.380: 7 0.380 - 0.475: 4 Chirality restraints: 2491 Sorted by residual: chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.24 0.16 2.00e-02 2.50e+03 6.36e+01 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.66e+01 chirality pdb=" C1 FUC d 3 " pdb=" O6 NAG d 1 " pdb=" C2 FUC d 3 " pdb=" O5 FUC d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.19e+01 ... (remaining 2488 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.101 2.00e-02 2.50e+03 8.44e-02 8.91e+01 pdb=" C7 NAG i 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 1 " 0.077 2.00e-02 2.50e+03 6.44e-02 5.19e+01 pdb=" C7 NAG e 1 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG e 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG e 1 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG e 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG k 2 " -0.067 2.00e-02 2.50e+03 5.65e-02 3.99e+01 pdb=" C7 NAG k 2 " 0.033 2.00e-02 2.50e+03 pdb=" C8 NAG k 2 " -0.056 2.00e-02 2.50e+03 pdb=" N2 NAG k 2 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG k 2 " 0.005 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 707 2.73 - 3.27: 14358 3.27 - 3.81: 25830 3.81 - 4.36: 36107 4.36 - 4.90: 55708 Nonbonded interactions: 132710 Sorted by model distance: nonbonded pdb=" O ASP E 293 " pdb="CA CA E 501 " model vdw 2.187 2.510 nonbonded pdb=" O HIS F 347 " pdb="CA CA F2000 " model vdw 2.217 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G2000 " model vdw 2.237 2.510 nonbonded pdb=" O HIS H 347 " pdb="CA CA H2000 " model vdw 2.280 2.510 nonbonded pdb=" O GLY F 345 " pdb="CA CA F2000 " model vdw 2.291 2.510 ... (remaining 132705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = (chain 'E' and resid 82 through 501) selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9231 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 : 13.633 89.946 5083 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 1778 helix: -0.48 (0.90), residues: 24 sheet: 0.26 (0.19), residues: 681 loop : -1.10 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG G 156 TYR 0.076 0.014 TYR H 423 PHE 0.051 0.012 PHE E 205 TRP 0.078 0.015 TRP G 115 HIS 0.033 0.007 HIS E 347 Details of bonding type rmsd/Z covalent geometry : bond 0.01427 / 0.98 (15206) covalent geometry : angle 1.67132 / 1.07 (20638) SS BOND : bond 0.05832 / 4.01 ( 38) SS BOND : angle 2.39306 / 1.65 ( 76) hydrogen bonds : bond 0.16176 / 10.65 ( 436) hydrogen bonds : angle 8.86013 / 6.12 ( 1176) link_ALPHA1-2 : bond 0.00772 / 0.38 ( 4) link_ALPHA1-2 : angle 4.45343 / 2.57 ( 12) link_ALPHA1-3 : bond 0.01533 / 0.93 ( 8) link_ALPHA1-3 : angle 2.99109 / 1.86 ( 24) link_ALPHA1-6 : bond 0.00918 / 0.57 ( 8) link_ALPHA1-6 : angle 2.84999 / 1.76 ( 24) link_BETA1-4 : bond 0.01445 / 0.93 ( 32) link_BETA1-4 : angle 4.17135 / 2.86 ( 96) link_BETA1-6 : bond 0.02133 / 1.12 ( 1) link_BETA1-6 : angle 4.17517 / 2.70 ( 3) link_NAG-ASN : bond 0.01456 / 0.95 ( 28) link_NAG-ASN : angle 4.55228 / 3.12 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.422 Fit side-chains REVERT: E 150 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8352 (mtp85) REVERT: G 199 LYS cc_start: 0.8992 (tttt) cc_final: 0.8715 (tptt) REVERT: B 4 MET cc_start: 0.8921 (mmm) cc_final: 0.8023 (mmm) REVERT: B 24 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8214 (mtm110) REVERT: B 27 GLN cc_start: 0.8411 (mt0) cc_final: 0.8185 (mp10) REVERT: B 92 ASN cc_start: 0.9181 (t0) cc_final: 0.8925 (t0) REVERT: C 100 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8287 (tpp80) REVERT: C 116 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 125 THR cc_start: 0.8948 (m) cc_final: 0.8512 (p) REVERT: H 465 ASN cc_start: 0.9066 (m-40) cc_final: 0.8798 (m110) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.6476 time to fit residues: 98.7181 Evaluate side-chains 101 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3271 r_free = 0.3271 target = 0.091119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.067191 restraints weight = 22303.570| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.37 r_work: 0.2729 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15325 Z= 0.160 Angle : 0.702 7.393 20957 Z= 0.366 Chirality : 0.048 0.189 2491 Planarity : 0.004 0.033 2549 Dihedral : 6.375 25.000 1940 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.02 % Favored : 97.75 % Rotamer: Outliers : 0.90 % Allowed : 6.78 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1778 helix: 0.01 (0.94), residues: 24 sheet: 0.55 (0.19), residues: 656 loop : -0.56 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 403 TYR 0.022 0.002 TYR B 91 PHE 0.016 0.002 PHE E 132 TRP 0.022 0.002 TRP H 178 HIS 0.008 0.001 HIS E 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (15206) covalent geometry : angle 0.67481 / 0.36 (20638) SS BOND : bond 0.00291 / 0.16 ( 38) SS BOND : angle 0.73411 / 0.51 ( 76) hydrogen bonds : bond 0.04781 / 3.38 ( 436) hydrogen bonds : angle 7.11614 / 4.94 ( 1176) link_ALPHA1-2 : bond 0.00336 / 0.16 ( 4) link_ALPHA1-2 : angle 1.54456 / 0.82 ( 12) link_ALPHA1-3 : bond 0.00637 / 0.36 ( 8) link_ALPHA1-3 : angle 1.56763 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00443 / 0.27 ( 8) link_ALPHA1-6 : angle 1.22159 / 0.75 ( 24) link_BETA1-4 : bond 0.00387 / 0.25 ( 32) link_BETA1-4 : angle 1.61509 / 1.11 ( 96) link_BETA1-6 : bond 0.01006 / 0.53 ( 1) link_BETA1-6 : angle 1.88181 / 0.94 ( 3) link_NAG-ASN : bond 0.00227 / 0.14 ( 28) link_NAG-ASN : angle 2.42269 / 1.66 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: E 381 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7628 (mt-10) REVERT: G 83 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7580 (tp30) REVERT: G 199 LYS cc_start: 0.8446 (tttt) cc_final: 0.7986 (tptp) REVERT: B 24 ARG cc_start: 0.7860 (ttt-90) cc_final: 0.7564 (mtp-110) REVERT: B 27 GLN cc_start: 0.8058 (mt0) cc_final: 0.7621 (mp10) REVERT: B 70 GLU cc_start: 0.7478 (tp30) cc_final: 0.7065 (mm-30) REVERT: B 92 ASN cc_start: 0.8635 (t0) cc_final: 0.8256 (t0) REVERT: C 78 THR cc_start: 0.8141 (m) cc_final: 0.7541 (p) REVERT: C 125 THR cc_start: 0.8910 (m) cc_final: 0.8673 (p) REVERT: F 199 LYS cc_start: 0.8299 (mttt) cc_final: 0.8065 (mttm) REVERT: H 221 GLU cc_start: 0.8169 (tt0) cc_final: 0.7906 (mt-10) REVERT: H 387 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8654 (mtpp) REVERT: H 465 ASN cc_start: 0.8839 (m-40) cc_final: 0.8416 (m110) REVERT: H 467 MET cc_start: 0.7888 (ptm) cc_final: 0.7678 (ptm) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.5497 time to fit residues: 77.5771 Evaluate side-chains 107 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0020 chunk 10 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN ** G 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.065579 restraints weight = 22756.154| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.36 r_work: 0.2709 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15325 Z= 0.248 Angle : 0.707 7.116 20957 Z= 0.365 Chirality : 0.048 0.213 2491 Planarity : 0.004 0.039 2549 Dihedral : 6.153 25.246 1940 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.49 % Allowed : 7.69 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1778 helix: 0.03 (0.98), residues: 24 sheet: 0.43 (0.19), residues: 677 loop : -0.58 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 85 TYR 0.021 0.002 TYR B 91 PHE 0.016 0.002 PHE E 410 TRP 0.021 0.002 TRP H 178 HIS 0.005 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (15206) covalent geometry : angle 0.67589 / 0.36 (20638) SS BOND : bond 0.00356 / 0.19 ( 38) SS BOND : angle 1.16281 / 0.83 ( 76) hydrogen bonds : bond 0.04934 / 3.45 ( 436) hydrogen bonds : angle 6.96750 / 4.83 ( 1176) link_ALPHA1-2 : bond 0.00083 / 0.04 ( 4) link_ALPHA1-2 : angle 1.99279 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00315 / 0.17 ( 8) link_ALPHA1-3 : angle 1.77532 / 1.10 ( 24) link_ALPHA1-6 : bond 0.00245 / 0.15 ( 8) link_ALPHA1-6 : angle 1.54019 / 0.94 ( 24) link_BETA1-4 : bond 0.00385 / 0.25 ( 32) link_BETA1-4 : angle 1.62253 / 1.08 ( 96) link_BETA1-6 : bond 0.01160 / 0.61 ( 1) link_BETA1-6 : angle 1.28993 / 0.70 ( 3) link_NAG-ASN : bond 0.00345 / 0.21 ( 28) link_NAG-ASN : angle 2.44226 / 1.68 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 241 MET cc_start: 0.9419 (mtp) cc_final: 0.9102 (mtm) REVERT: E 381 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7767 (mt-10) REVERT: G 199 LYS cc_start: 0.8437 (tttt) cc_final: 0.7982 (tptp) REVERT: B 24 ARG cc_start: 0.7921 (ttt-90) cc_final: 0.7560 (mtp-110) REVERT: B 27 GLN cc_start: 0.8114 (mt0) cc_final: 0.7621 (mp10) REVERT: B 70 GLU cc_start: 0.7806 (tp30) cc_final: 0.7348 (tp30) REVERT: B 92 ASN cc_start: 0.8618 (t0) cc_final: 0.8224 (t0) REVERT: B 98 THR cc_start: 0.8901 (m) cc_final: 0.8405 (p) REVERT: C 23 LYS cc_start: 0.8398 (mttp) cc_final: 0.8183 (mtpm) REVERT: C 39 GLN cc_start: 0.7474 (tt0) cc_final: 0.7262 (tt0) REVERT: C 98 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7433 (ttp80) REVERT: C 117 ASN cc_start: 0.8575 (m110) cc_final: 0.7852 (m110) REVERT: C 125 THR cc_start: 0.8925 (m) cc_final: 0.8655 (p) REVERT: F 199 LYS cc_start: 0.8404 (mttt) cc_final: 0.8187 (mttm) REVERT: H 221 GLU cc_start: 0.8331 (tt0) cc_final: 0.8039 (mt-10) REVERT: H 387 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8666 (mtpp) REVERT: H 465 ASN cc_start: 0.8827 (m-40) cc_final: 0.8402 (m110) REVERT: H 467 MET cc_start: 0.7911 (ptm) cc_final: 0.7623 (ptm) outliers start: 23 outliers final: 9 residues processed: 127 average time/residue: 0.5300 time to fit residues: 74.2179 Evaluate side-chains 118 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Chi-restraints excluded: chain H residue 443 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 74 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067026 restraints weight = 22604.686| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.35 r_work: 0.2742 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15325 Z= 0.169 Angle : 0.641 8.553 20957 Z= 0.330 Chirality : 0.046 0.209 2491 Planarity : 0.003 0.040 2549 Dihedral : 5.793 26.008 1940 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.14 % Favored : 97.64 % Rotamer: Outliers : 1.23 % Allowed : 8.98 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1778 helix: 0.16 (0.98), residues: 24 sheet: 0.45 (0.19), residues: 668 loop : -0.53 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 152 TYR 0.019 0.002 TYR B 91 PHE 0.016 0.002 PHE E 410 TRP 0.018 0.002 TRP H 178 HIS 0.004 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (15206) covalent geometry : angle 0.61528 / 0.33 (20638) SS BOND : bond 0.00267 / 0.14 ( 38) SS BOND : angle 0.99383 / 0.71 ( 76) hydrogen bonds : bond 0.04298 / 3.02 ( 436) hydrogen bonds : angle 6.68806 / 4.65 ( 1176) link_ALPHA1-2 : bond 0.00190 / 0.09 ( 4) link_ALPHA1-2 : angle 1.80069 / 0.95 ( 12) link_ALPHA1-3 : bond 0.00422 / 0.24 ( 8) link_ALPHA1-3 : angle 1.54359 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00303 / 0.19 ( 8) link_ALPHA1-6 : angle 1.46563 / 0.89 ( 24) link_BETA1-4 : bond 0.00392 / 0.25 ( 32) link_BETA1-4 : angle 1.43670 / 0.97 ( 96) link_BETA1-6 : bond 0.01138 / 0.60 ( 1) link_BETA1-6 : angle 1.27291 / 0.69 ( 3) link_NAG-ASN : bond 0.00182 / 0.11 ( 28) link_NAG-ASN : angle 2.11275 / 1.45 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 241 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9161 (mtm) REVERT: E 381 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7793 (mt-10) REVERT: G 199 LYS cc_start: 0.8474 (tttt) cc_final: 0.8016 (tptp) REVERT: G 344 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: B 24 ARG cc_start: 0.7843 (ttt-90) cc_final: 0.7587 (mtp-110) REVERT: B 70 GLU cc_start: 0.7854 (tp30) cc_final: 0.7425 (mm-30) REVERT: B 92 ASN cc_start: 0.8585 (t0) cc_final: 0.8208 (t0) REVERT: B 98 THR cc_start: 0.8966 (m) cc_final: 0.8448 (p) REVERT: C 23 LYS cc_start: 0.8465 (mttp) cc_final: 0.8217 (mtpm) REVERT: C 67 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7445 (ptm160) REVERT: C 78 THR cc_start: 0.8278 (m) cc_final: 0.7486 (p) REVERT: C 125 THR cc_start: 0.8963 (m) cc_final: 0.8685 (p) REVERT: F 199 LYS cc_start: 0.8320 (mttt) cc_final: 0.8091 (mttm) REVERT: H 221 GLU cc_start: 0.8305 (tt0) cc_final: 0.8018 (mt-10) REVERT: H 387 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8658 (mtpp) REVERT: H 400 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7687 (ptm160) REVERT: H 465 ASN cc_start: 0.8826 (m-40) cc_final: 0.8425 (m110) REVERT: H 467 MET cc_start: 0.7781 (ptm) cc_final: 0.7569 (ptm) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.5717 time to fit residues: 77.5015 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 : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 241 MET 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 67 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067927 restraints weight = 22640.292| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.36 r_work: 0.2756 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15325 Z= 0.142 Angle : 0.614 8.853 20957 Z= 0.315 Chirality : 0.045 0.222 2491 Planarity : 0.003 0.041 2549 Dihedral : 5.544 23.021 1940 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.25 % Favored : 97.53 % Rotamer: Outliers : 1.36 % Allowed : 9.56 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1778 helix: 0.21 (0.99), residues: 24 sheet: 0.42 (0.19), residues: 678 loop : -0.45 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 98 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.017 0.001 TRP H 178 HIS 0.004 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15206) covalent geometry : angle 0.59090 / 0.31 (20638) SS BOND : bond 0.00226 / 0.13 ( 38) SS BOND : angle 0.77225 / 0.54 ( 76) hydrogen bonds : bond 0.04009 / 2.81 ( 436) hydrogen bonds : angle 6.53841 / 4.55 ( 1176) link_ALPHA1-2 : bond 0.00265 / 0.13 ( 4) link_ALPHA1-2 : angle 1.72631 / 0.91 ( 12) link_ALPHA1-3 : bond 0.00480 / 0.27 ( 8) link_ALPHA1-3 : angle 1.51792 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00335 / 0.21 ( 8) link_ALPHA1-6 : angle 1.45273 / 0.89 ( 24) link_BETA1-4 : bond 0.00408 / 0.26 ( 32) link_BETA1-4 : angle 1.37441 / 0.93 ( 96) link_BETA1-6 : bond 0.01001 / 0.53 ( 1) link_BETA1-6 : angle 1.25234 / 0.67 ( 3) link_NAG-ASN : bond 0.00127 / 0.08 ( 28) link_NAG-ASN : angle 1.96089 / 1.34 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 241 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.9172 (mtm) REVERT: E 381 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7781 (mt-10) REVERT: G 199 LYS cc_start: 0.8435 (tttt) cc_final: 0.7996 (tptp) REVERT: G 344 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 5 THR cc_start: 0.8551 (m) cc_final: 0.8296 (p) REVERT: B 24 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7451 (mtp-110) REVERT: B 70 GLU cc_start: 0.7853 (tp30) cc_final: 0.7333 (mm-30) REVERT: B 92 ASN cc_start: 0.8542 (t0) cc_final: 0.8170 (t0) REVERT: B 98 THR cc_start: 0.8973 (m) cc_final: 0.8506 (p) REVERT: C 11 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8511 (t) REVERT: C 23 LYS cc_start: 0.8471 (mttp) cc_final: 0.8221 (mtpm) REVERT: C 67 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7407 (ptm160) REVERT: C 78 THR cc_start: 0.8329 (m) cc_final: 0.7610 (p) REVERT: C 98 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7480 (ttp80) REVERT: C 125 THR cc_start: 0.8941 (m) cc_final: 0.8554 (p) REVERT: F 199 LYS cc_start: 0.8347 (mttt) cc_final: 0.8132 (mttm) REVERT: H 221 GLU cc_start: 0.8308 (tt0) cc_final: 0.8021 (mt-10) REVERT: H 387 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8696 (mtpp) REVERT: H 400 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7666 (ptm160) REVERT: H 465 ASN cc_start: 0.8826 (m-40) cc_final: 0.8456 (m110) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.5265 time to fit residues: 71.4784 Evaluate side-chains 121 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 241 MET 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 91 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN G 441 ASN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070228 restraints weight = 22385.111| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.37 r_work: 0.2803 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15325 Z= 0.099 Angle : 0.566 10.994 20957 Z= 0.289 Chirality : 0.044 0.154 2491 Planarity : 0.003 0.042 2549 Dihedral : 5.094 21.264 1940 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.14 % Favored : 97.64 % Rotamer: Outliers : 1.23 % Allowed : 10.14 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1778 helix: 0.50 (0.99), residues: 24 sheet: 0.48 (0.19), residues: 677 loop : -0.28 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 98 TYR 0.015 0.001 TYR B 91 PHE 0.012 0.002 PHE F 410 TRP 0.015 0.001 TRP H 178 HIS 0.003 0.000 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (15206) covalent geometry : angle 0.54804 / 0.29 (20638) SS BOND : bond 0.00174 / 0.10 ( 38) SS BOND : angle 0.61353 / 0.42 ( 76) hydrogen bonds : bond 0.03478 / 2.43 ( 436) hydrogen bonds : angle 6.19151 / 4.30 ( 1176) link_ALPHA1-2 : bond 0.00464 / 0.22 ( 4) link_ALPHA1-2 : angle 1.48175 / 0.78 ( 12) link_ALPHA1-3 : bond 0.00617 / 0.36 ( 8) link_ALPHA1-3 : angle 1.36931 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00450 / 0.27 ( 8) link_ALPHA1-6 : angle 1.39953 / 0.86 ( 24) link_BETA1-4 : bond 0.00470 / 0.29 ( 32) link_BETA1-4 : angle 1.21404 / 0.84 ( 96) link_BETA1-6 : bond 0.00922 / 0.49 ( 1) link_BETA1-6 : angle 1.23037 / 0.66 ( 3) link_NAG-ASN : bond 0.00134 / 0.07 ( 28) link_NAG-ASN : angle 1.61386 / 1.09 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ASP cc_start: 0.8414 (p0) cc_final: 0.8174 (p0) REVERT: E 241 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9104 (mtm) REVERT: E 400 ARG cc_start: 0.8343 (ptp-110) cc_final: 0.7865 (ptm160) REVERT: G 199 LYS cc_start: 0.8452 (tttt) cc_final: 0.8036 (tptp) REVERT: B 5 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8472 (p) REVERT: B 24 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7496 (mtp-110) REVERT: B 70 GLU cc_start: 0.7884 (tp30) cc_final: 0.7402 (mm-30) REVERT: B 92 ASN cc_start: 0.8446 (t0) cc_final: 0.8051 (t0) REVERT: B 98 THR cc_start: 0.9014 (m) cc_final: 0.8594 (p) REVERT: C 23 LYS cc_start: 0.8476 (mttp) cc_final: 0.8224 (mtpm) REVERT: C 67 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7407 (ptm160) REVERT: C 78 THR cc_start: 0.8360 (m) cc_final: 0.7670 (p) REVERT: C 98 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7548 (ttp80) REVERT: C 125 THR cc_start: 0.8943 (m) cc_final: 0.8641 (p) REVERT: H 221 GLU cc_start: 0.8250 (tt0) cc_final: 0.7956 (mt-10) REVERT: H 387 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8643 (mtpp) REVERT: H 400 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7641 (ptm160) REVERT: H 465 ASN cc_start: 0.8801 (m-40) cc_final: 0.8488 (m110) outliers start: 19 outliers final: 8 residues processed: 138 average time/residue: 0.5120 time to fit residues: 78.2257 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 241 MET Chi-restraints excluded: chain G residue 148 THR 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 F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 153 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068375 restraints weight = 22723.678| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.37 r_work: 0.2750 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15325 Z= 0.165 Angle : 0.599 8.941 20957 Z= 0.307 Chirality : 0.045 0.154 2491 Planarity : 0.004 0.043 2549 Dihedral : 5.287 22.228 1940 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.59 % Favored : 97.19 % Rotamer: Outliers : 1.29 % Allowed : 11.11 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.19), residues: 1778 helix: 0.65 (1.04), residues: 24 sheet: 0.42 (0.19), residues: 677 loop : -0.33 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 98 TYR 0.017 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.014 0.001 TRP H 178 HIS 0.003 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (15206) covalent geometry : angle 0.57487 / 0.30 (20638) SS BOND : bond 0.00245 / 0.14 ( 38) SS BOND : angle 0.95385 / 0.68 ( 76) hydrogen bonds : bond 0.03923 / 2.73 ( 436) hydrogen bonds : angle 6.38981 / 4.44 ( 1176) link_ALPHA1-2 : bond 0.00238 / 0.12 ( 4) link_ALPHA1-2 : angle 1.68672 / 0.89 ( 12) link_ALPHA1-3 : bond 0.00368 / 0.21 ( 8) link_ALPHA1-3 : angle 1.55464 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00282 / 0.17 ( 8) link_ALPHA1-6 : angle 1.49153 / 0.91 ( 24) link_BETA1-4 : bond 0.00358 / 0.23 ( 32) link_BETA1-4 : angle 1.38488 / 0.94 ( 96) link_BETA1-6 : bond 0.00877 / 0.46 ( 1) link_BETA1-6 : angle 1.23035 / 0.69 ( 3) link_NAG-ASN : bond 0.00176 / 0.11 ( 28) link_NAG-ASN : angle 1.86467 / 1.28 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 150 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: E 400 ARG cc_start: 0.8389 (ptp-110) cc_final: 0.7903 (ptm160) REVERT: G 199 LYS cc_start: 0.8444 (tttt) cc_final: 0.8021 (tptt) REVERT: B 24 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7677 (mtp-110) REVERT: B 92 ASN cc_start: 0.8516 (t0) cc_final: 0.8113 (t0) REVERT: B 98 THR cc_start: 0.9023 (m) cc_final: 0.8615 (p) REVERT: C 11 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (t) REVERT: C 23 LYS cc_start: 0.8507 (mttp) cc_final: 0.8255 (mtpm) REVERT: C 67 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7402 (ptm160) REVERT: C 78 THR cc_start: 0.8387 (m) cc_final: 0.7688 (p) REVERT: C 98 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7954 (ptm160) REVERT: C 125 THR cc_start: 0.8945 (m) cc_final: 0.8535 (p) REVERT: H 221 GLU cc_start: 0.8325 (tt0) cc_final: 0.8041 (mt-10) REVERT: H 387 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8644 (mtpp) REVERT: H 400 ARG cc_start: 0.8150 (ptp-110) cc_final: 0.7672 (ptm160) REVERT: H 465 ASN cc_start: 0.8808 (m-40) cc_final: 0.8480 (m110) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.5461 time to fit residues: 70.5533 Evaluate side-chains 116 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3299 r_free = 0.3299 target = 0.092318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.068816 restraints weight = 22712.793| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.38 r_work: 0.2758 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15325 Z= 0.138 Angle : 0.585 9.593 20957 Z= 0.300 Chirality : 0.044 0.170 2491 Planarity : 0.003 0.042 2549 Dihedral : 5.226 21.974 1940 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.31 % Favored : 97.47 % Rotamer: Outliers : 1.16 % Allowed : 11.56 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1778 helix: 0.82 (1.08), residues: 24 sheet: 0.44 (0.19), residues: 677 loop : -0.32 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 98 TYR 0.016 0.002 TYR B 91 PHE 0.014 0.002 PHE E 410 TRP 0.018 0.001 TRP C 118 HIS 0.003 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (15206) covalent geometry : angle 0.56372 / 0.30 (20638) SS BOND : bond 0.00219 / 0.13 ( 38) SS BOND : angle 0.81166 / 0.57 ( 76) hydrogen bonds : bond 0.03799 / 2.65 ( 436) hydrogen bonds : angle 6.32787 / 4.41 ( 1176) link_ALPHA1-2 : bond 0.00290 / 0.14 ( 4) link_ALPHA1-2 : angle 1.64813 / 0.87 ( 12) link_ALPHA1-3 : bond 0.00431 / 0.25 ( 8) link_ALPHA1-3 : angle 1.48911 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00317 / 0.19 ( 8) link_ALPHA1-6 : angle 1.46687 / 0.90 ( 24) link_BETA1-4 : bond 0.00388 / 0.24 ( 32) link_BETA1-4 : angle 1.32362 / 0.90 ( 96) link_BETA1-6 : bond 0.00897 / 0.47 ( 1) link_BETA1-6 : angle 1.22704 / 0.68 ( 3) link_NAG-ASN : bond 0.00120 / 0.07 ( 28) link_NAG-ASN : angle 1.76085 / 1.20 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 241 MET cc_start: 0.9425 (mtp) cc_final: 0.9124 (mtm) REVERT: G 199 LYS cc_start: 0.8402 (tttt) cc_final: 0.7989 (tptt) REVERT: B 4 MET cc_start: 0.8881 (mmm) cc_final: 0.8634 (mmm) REVERT: B 5 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8305 (p) REVERT: B 24 ARG cc_start: 0.7891 (ttt-90) cc_final: 0.7623 (mtp-110) REVERT: B 92 ASN cc_start: 0.8547 (t0) cc_final: 0.8169 (t0) REVERT: B 98 THR cc_start: 0.9032 (m) cc_final: 0.8629 (p) REVERT: C 11 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8504 (t) REVERT: C 23 LYS cc_start: 0.8506 (mttp) cc_final: 0.8255 (mtpm) REVERT: C 67 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7442 (ptm160) REVERT: C 78 THR cc_start: 0.8380 (m) cc_final: 0.7685 (p) REVERT: C 125 THR cc_start: 0.8931 (m) cc_final: 0.8479 (p) REVERT: H 221 GLU cc_start: 0.8299 (tt0) cc_final: 0.8016 (mt-10) REVERT: H 387 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (mtpp) REVERT: H 400 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7660 (ptm160) REVERT: H 465 ASN cc_start: 0.8802 (m-40) cc_final: 0.8476 (m110) outliers start: 18 outliers final: 9 residues processed: 117 average time/residue: 0.5592 time to fit residues: 72.2664 Evaluate side-chains 117 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 10 THR 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 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN G 441 ASN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.064877 restraints weight = 23088.096| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.38 r_work: 0.2681 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 15325 Z= 0.338 Angle : 0.719 9.968 20957 Z= 0.367 Chirality : 0.050 0.255 2491 Planarity : 0.004 0.044 2549 Dihedral : 5.814 27.047 1940 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.98 % Favored : 96.79 % Rotamer: Outliers : 1.10 % Allowed : 11.43 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1778 helix: 0.54 (1.11), residues: 24 sheet: 0.29 (0.19), residues: 658 loop : -0.57 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 98 TYR 0.021 0.003 TYR B 91 PHE 0.018 0.003 PHE E 410 TRP 0.016 0.002 TRP H 178 HIS 0.004 0.002 HIS E 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.34 (15206) covalent geometry : angle 0.68820 / 0.36 (20638) SS BOND : bond 0.00419 / 0.26 ( 38) SS BOND : angle 1.24657 / 0.94 ( 76) hydrogen bonds : bond 0.04854 / 3.37 ( 436) hydrogen bonds : angle 6.83426 / 4.75 ( 1176) link_ALPHA1-2 : bond 0.00230 / 0.10 ( 4) link_ALPHA1-2 : angle 2.09894 / 1.13 ( 12) link_ALPHA1-3 : bond 0.00201 / 0.11 ( 8) link_ALPHA1-3 : angle 1.95409 / 1.20 ( 24) link_ALPHA1-6 : bond 0.00143 / 0.09 ( 8) link_ALPHA1-6 : angle 1.66002 / 1.02 ( 24) link_BETA1-4 : bond 0.00285 / 0.19 ( 32) link_BETA1-4 : angle 1.68182 / 1.11 ( 96) link_BETA1-6 : bond 0.00855 / 0.45 ( 1) link_BETA1-6 : angle 1.21102 / 0.74 ( 3) link_NAG-ASN : bond 0.00555 / 0.33 ( 28) link_NAG-ASN : angle 2.33293 / 1.61 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 241 MET cc_start: 0.9455 (mtp) cc_final: 0.9219 (mtm) REVERT: G 199 LYS cc_start: 0.8454 (tttt) cc_final: 0.7996 (tptt) REVERT: G 344 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 4 MET cc_start: 0.8959 (mmm) cc_final: 0.8751 (mmm) REVERT: B 24 ARG cc_start: 0.7907 (ttt-90) cc_final: 0.7560 (mtp-110) REVERT: B 42 GLN cc_start: 0.8178 (mt0) cc_final: 0.7751 (mp10) REVERT: B 70 GLU cc_start: 0.7878 (tp30) cc_final: 0.7416 (mm-30) REVERT: B 73 LEU cc_start: 0.8820 (tt) cc_final: 0.8597 (tm) REVERT: B 92 ASN cc_start: 0.8661 (t0) cc_final: 0.8266 (t0) REVERT: B 98 THR cc_start: 0.9023 (m) cc_final: 0.8585 (p) REVERT: C 23 LYS cc_start: 0.8503 (mttp) cc_final: 0.8270 (mtpm) REVERT: C 67 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7376 (ptm160) REVERT: C 125 THR cc_start: 0.8904 (m) cc_final: 0.8533 (p) REVERT: H 221 GLU cc_start: 0.8379 (tt0) cc_final: 0.8115 (mt-10) REVERT: H 387 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8490 (mtmm) REVERT: H 400 ARG cc_start: 0.8208 (ptp-110) cc_final: 0.7740 (ptm160) REVERT: H 465 ASN cc_start: 0.8838 (m-40) cc_final: 0.8524 (m110) outliers start: 17 outliers final: 11 residues processed: 118 average time/residue: 0.5655 time to fit residues: 73.6118 Evaluate side-chains 115 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 387 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 141 ASN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.068392 restraints weight = 22750.068| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.38 r_work: 0.2763 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15325 Z= 0.118 Angle : 0.591 10.208 20957 Z= 0.303 Chirality : 0.044 0.178 2491 Planarity : 0.003 0.042 2549 Dihedral : 5.279 25.597 1940 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.53 % Favored : 97.24 % Rotamer: Outliers : 0.65 % Allowed : 12.14 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1778 helix: 0.70 (1.08), residues: 24 sheet: 0.35 (0.19), residues: 657 loop : -0.42 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 98 TYR 0.017 0.002 TYR B 91 PHE 0.012 0.002 PHE E 410 TRP 0.018 0.001 TRP F 178 HIS 0.004 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (15206) covalent geometry : angle 0.57273 / 0.30 (20638) SS BOND : bond 0.00248 / 0.17 ( 38) SS BOND : angle 0.84936 / 0.69 ( 76) hydrogen bonds : bond 0.03723 / 2.62 ( 436) hydrogen bonds : angle 6.33632 / 4.41 ( 1176) link_ALPHA1-2 : bond 0.00335 / 0.16 ( 4) link_ALPHA1-2 : angle 1.58899 / 0.84 ( 12) link_ALPHA1-3 : bond 0.00555 / 0.32 ( 8) link_ALPHA1-3 : angle 1.39008 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00377 / 0.23 ( 8) link_ALPHA1-6 : angle 1.41296 / 0.86 ( 24) link_BETA1-4 : bond 0.00442 / 0.27 ( 32) link_BETA1-4 : angle 1.22328 / 0.83 ( 96) link_BETA1-6 : bond 0.00865 / 0.46 ( 1) link_BETA1-6 : angle 1.17671 / 0.65 ( 3) link_NAG-ASN : bond 0.00176 / 0.10 ( 28) link_NAG-ASN : angle 1.64602 / 1.12 ( 84) ********************** 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 113 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 199 LYS cc_start: 0.8396 (tttt) cc_final: 0.7979 (tptt) REVERT: B 4 MET cc_start: 0.8914 (mmm) cc_final: 0.8623 (mmm) REVERT: B 5 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 24 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7484 (mtp-110) REVERT: B 70 GLU cc_start: 0.7868 (tp30) cc_final: 0.7358 (mm-30) REVERT: B 92 ASN cc_start: 0.8574 (t0) cc_final: 0.8194 (t0) REVERT: B 98 THR cc_start: 0.8973 (m) cc_final: 0.8558 (p) REVERT: C 23 LYS cc_start: 0.8497 (mttp) cc_final: 0.8236 (mtpm) REVERT: C 67 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7456 (ptm160) REVERT: C 78 THR cc_start: 0.8410 (m) cc_final: 0.7683 (p) REVERT: C 98 ARG cc_start: 0.8323 (ptm160) cc_final: 0.7116 (ttp80) REVERT: C 117 ASN cc_start: 0.8306 (m110) cc_final: 0.7600 (p0) REVERT: C 125 THR cc_start: 0.8910 (m) cc_final: 0.8548 (p) REVERT: F 431 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8766 (pttm) REVERT: H 221 GLU cc_start: 0.8340 (tt0) cc_final: 0.8060 (mt-10) REVERT: H 387 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8504 (mtmm) REVERT: H 400 ARG cc_start: 0.8161 (ptp-110) cc_final: 0.7669 (ptm160) REVERT: H 465 ASN cc_start: 0.8809 (m-40) cc_final: 0.8480 (m110) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.5166 time to fit residues: 63.1849 Evaluate side-chains 113 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3240 r_free = 0.3240 target = 0.088546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.064776 restraints weight = 23048.037| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.38 r_work: 0.2678 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 15325 Z= 0.356 Angle : 0.726 9.300 20957 Z= 0.370 Chirality : 0.050 0.237 2491 Planarity : 0.004 0.048 2549 Dihedral : 5.781 26.597 1940 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.21 % Favored : 96.57 % Rotamer: Outliers : 0.84 % Allowed : 12.02 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.93 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1778 helix: 0.51 (1.10), residues: 24 sheet: 0.26 (0.19), residues: 679 loop : -0.60 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 98 TYR 0.021 0.003 TYR B 91 PHE 0.020 0.003 PHE E 410 TRP 0.016 0.002 TRP H 178 HIS 0.005 0.001 HIS G 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.36 (15206) covalent geometry : angle 0.69574 / 0.36 (20638) SS BOND : bond 0.00434 / 0.27 ( 38) SS BOND : angle 1.26289 / 0.97 ( 76) hydrogen bonds : bond 0.04885 / 3.40 ( 436) hydrogen bonds : angle 6.82362 / 4.74 ( 1176) link_ALPHA1-2 : bond 0.00228 / 0.10 ( 4) link_ALPHA1-2 : angle 2.03312 / 1.09 ( 12) link_ALPHA1-3 : bond 0.00225 / 0.13 ( 8) link_ALPHA1-3 : angle 1.93581 / 1.19 ( 24) link_ALPHA1-6 : bond 0.00146 / 0.09 ( 8) link_ALPHA1-6 : angle 1.66093 / 1.01 ( 24) link_BETA1-4 : bond 0.00287 / 0.19 ( 32) link_BETA1-4 : angle 1.67038 / 1.10 ( 96) link_BETA1-6 : bond 0.00878 / 0.46 ( 1) link_BETA1-6 : angle 1.19564 / 0.74 ( 3) link_NAG-ASN : bond 0.00585 / 0.35 ( 28) link_NAG-ASN : angle 2.30017 / 1.59 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.67 seconds wall clock time: 81 minutes 29.33 seconds (4889.33 seconds total)