Starting phenix.real_space_refine on Sat Jul 4 05:26:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3o_29706/07_2026/8g3o_29706.map" } resolution = 3.1 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11416 2.51 5 N 3132 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 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: 18487 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} 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: "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: "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: "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: "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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 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: "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: "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: "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: "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: "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: "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: "5" 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: "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: "m" 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: "u" 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: "G" 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.25 Number of scatterers: 18487 At special positions: 0 Unit cell: (112.88, 140.27, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3825 8.00 N 3132 7.00 C 11416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.07 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.06 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=2.08 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.06 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.07 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.02 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.09 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.07 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=2.12 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.06 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.06 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.08 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.13 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.09 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.06 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.08 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.05 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.12 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 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 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 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 w 1 " - " NAG w 2 " BETA1-6 " NAG 5 1 " - " FUC 5 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG e 1 " - " FUC e 3 " " NAG m 1 " - " FUC m 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG 1 1 " - " ASN J 86 " " NAG 2 1 " - " ASN J 146 " " NAG 3 1 " - " ASN J 200 " " NAG 4 1 " - " ASN J 234 " " NAG 5 1 " - " ASN J 245 " " NAG 7 1 " - " ASN J 367 " " NAG a 1 " - " ASN G 86 " " NAG b 1 " - " ASN G 146 " " NAG c 1 " - " ASN G 200 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 245 " " NAG g 1 " - " ASN G 367 " " NAG i 1 " - " ASN H 86 " " NAG j 1 " - " ASN H 146 " " NAG k 1 " - " ASN H 200 " " NAG l 1 " - " ASN H 234 " " NAG m 1 " - " ASN H 245 " " NAG o 1 " - " ASN H 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 4.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.792A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.780A pdb=" N SER D 83 " --> pdb=" O SER D 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 'I' and resid 79 through 83 removed outlier: 3.785A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.736A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.740A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.731A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.629A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.632A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.595A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.631A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.573A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.470A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.802A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.447A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.414A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.485A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.764A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.782A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.840A 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: 4.778A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.893A 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: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.427A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.450A 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: 5.404A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.461A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.543A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.750A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.346A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.479A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.772A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.123A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.429A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.494A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.815A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.373A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.796A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.117A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.435A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.458A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.789A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.357A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3171 1.32 - 1.45: 5346 1.45 - 1.58: 10224 1.58 - 1.71: 0 1.71 - 1.85: 134 Bond restraints: 18875 Sorted by residual: bond pdb=" C SER J 404 " pdb=" O SER J 404 " ideal model delta sigma weight residual 1.235 1.298 -0.062 1.26e-02 6.30e+03 2.45e+01 bond pdb=" C LYS G 350 " pdb=" O LYS G 350 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.20e-02 6.94e+03 1.97e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" N GLY G 286 " pdb=" CA GLY G 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" C PRO H 90 " pdb=" O PRO H 90 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.73e+01 ... (remaining 18870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 20936 2.21 - 4.42: 4275 4.42 - 6.63: 365 6.63 - 8.84: 33 8.84 - 11.04: 8 Bond angle restraints: 25617 Sorted by residual: angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.53e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" CA ASP H 125 " pdb=" CB ASP H 125 " pdb=" CG ASP H 125 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.00e+00 1.00e+00 3.38e+01 ... (remaining 25612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9952 18.00 - 35.99: 475 35.99 - 53.99: 108 53.99 - 71.99: 38 71.99 - 89.98: 26 Dihedral angle restraints: 10599 sinusoidal: 4148 harmonic: 6451 Sorted by residual: dihedral pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N ASN J 245 " pdb=" CA ASN J 245 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP J 127 " pdb=" C ASP J 127 " pdb=" N LYS J 128 " pdb=" CA LYS J 128 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY J 297 " pdb=" C GLY J 297 " pdb=" N SER J 298 " pdb=" CA SER J 298 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 10596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2423 0.120 - 0.240: 576 0.240 - 0.361: 11 0.361 - 0.481: 5 0.481 - 0.601: 1 Chirality restraints: 3016 Sorted by residual: chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.21e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.96e+01 chirality pdb=" C1 MAN 3 4 " pdb=" O3 BMA 3 3 " pdb=" C2 MAN 3 4 " pdb=" O5 MAN 3 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 3013 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.076 2.00e-02 2.50e+03 6.44e-02 5.18e+01 pdb=" C7 NAG c 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.098 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 1 " -0.074 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG r 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG r 1 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG r 1 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG r 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 281 " -0.084 2.00e-02 2.50e+03 4.45e-02 3.97e+01 pdb=" CG TYR J 281 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR J 281 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR J 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR J 281 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 281 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR J 281 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR J 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1410 2.75 - 3.29: 18460 3.29 - 3.83: 30748 3.83 - 4.36: 42465 4.36 - 4.90: 67681 Nonbonded interactions: 160764 Sorted by model distance: nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.218 2.510 nonbonded pdb=" OD2 ASP B 324 " pdb="CA CA B2000 " model vdw 2.239 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.252 2.510 nonbonded pdb=" OD2 ASP H 324 " pdb="CA CA H2000 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 160759 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 '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '5' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'G' and resid 82 through 501) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } 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: 11.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.060 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 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 0.102 18993 Z= 1.037 Angle : 1.752 14.536 25929 Z= 1.116 Chirality : 0.094 0.601 3016 Planarity : 0.010 0.064 3198 Dihedral : 12.942 89.983 6365 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.77 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2252 helix: -1.12 (0.70), residues: 24 sheet: 0.04 (0.16), residues: 925 loop : -0.70 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.003 ARG H 288 TYR 0.084 0.013 TYR J 281 PHE 0.057 0.013 PHE G 205 TRP 0.060 0.013 TRP B 458 HIS 0.046 0.007 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.01489 / 1.03 (18875) covalent geometry : angle 1.70803 / 1.11 (25617) SS BOND : bond 0.04676 / 3.08 ( 42) SS BOND : angle 2.40405 / 1.62 ( 84) hydrogen bonds : bond 0.16151 / 10.67 ( 572) hydrogen bonds : angle 8.58427 / 6.04 ( 1518) link_ALPHA1-2 : bond 0.00289 / 0.15 ( 4) link_ALPHA1-2 : angle 4.89940 / 2.95 ( 12) link_ALPHA1-3 : bond 0.01904 / 1.20 ( 8) link_ALPHA1-3 : angle 2.87221 / 1.86 ( 24) link_ALPHA1-6 : bond 0.01550 / 0.90 ( 8) link_ALPHA1-6 : angle 3.20270 / 2.22 ( 24) link_BETA1-4 : bond 0.01548 / 1.18 ( 28) link_BETA1-4 : angle 4.16160 / 2.97 ( 84) link_BETA1-6 : bond 0.01223 / 0.60 ( 4) link_BETA1-6 : angle 3.27205 / 1.92 ( 12) link_NAG-ASN : bond 0.01782 / 1.23 ( 24) link_NAG-ASN : angle 5.35011 / 4.00 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.7815 (m-30) cc_final: 0.6939 (m-30) REVERT: F 11 LEU cc_start: 0.8017 (tp) cc_final: 0.7664 (tt) REVERT: F 75 ILE cc_start: 0.9128 (mt) cc_final: 0.8911 (mp) REVERT: F 79 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7050 (mp10) REVERT: A 43 GLN cc_start: 0.8830 (tt0) cc_final: 0.8480 (mt0) REVERT: A 65 GLN cc_start: 0.8812 (tt0) cc_final: 0.8611 (tp-100) REVERT: D 42 GLN cc_start: 0.8890 (mt0) cc_final: 0.8662 (mt0) REVERT: D 75 ILE cc_start: 0.9472 (mt) cc_final: 0.9241 (tt) REVERT: C 23 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8999 (tttp) REVERT: C 36 TRP cc_start: 0.9275 (m100) cc_final: 0.8952 (m100) REVERT: C 64 PHE cc_start: 0.8594 (m-80) cc_final: 0.8256 (m-10) REVERT: C 81 MET cc_start: 0.8256 (tmm) cc_final: 0.8035 (tmm) REVERT: C 90 ASP cc_start: 0.7477 (m-30) cc_final: 0.6935 (m-30) REVERT: C 93 VAL cc_start: 0.9147 (t) cc_final: 0.8892 (p) REVERT: C 102 ASP cc_start: 0.9066 (p0) cc_final: 0.8703 (p0) REVERT: I 4 MET cc_start: 0.8606 (mmm) cc_final: 0.7799 (mmm) REVERT: I 6 GLN cc_start: 0.8277 (tt0) cc_final: 0.7883 (tt0) REVERT: I 42 GLN cc_start: 0.7786 (mt0) cc_final: 0.7228 (mp10) REVERT: I 82 ASP cc_start: 0.7994 (m-30) cc_final: 0.7645 (m-30) REVERT: I 109 ARG cc_start: 0.6332 (ptm160) cc_final: 0.5263 (pmt-80) REVERT: H 141 ASN cc_start: 0.9366 (t0) cc_final: 0.8904 (p0) REVERT: B 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8671 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1764 time to fit residues: 74.0174 Evaluate side-chains 182 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 GLN E 65 GLN A 120 GLN D 6 GLN C 6 GLN G 274 HIS G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.059952 restraints weight = 43490.018| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.86 r_work: 0.2845 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18993 Z= 0.144 Angle : 0.722 10.753 25929 Z= 0.377 Chirality : 0.047 0.323 3016 Planarity : 0.004 0.030 3198 Dihedral : 5.886 23.574 2466 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2252 helix: -0.67 (0.85), residues: 24 sheet: -0.02 (0.16), residues: 948 loop : -0.15 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 106 TYR 0.015 0.002 TYR H 121 PHE 0.017 0.002 PHE B 410 TRP 0.023 0.002 TRP G 178 HIS 0.007 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (18875) covalent geometry : angle 0.69100 / 0.37 (25617) SS BOND : bond 0.00298 / 0.19 ( 42) SS BOND : angle 1.34465 / 1.11 ( 84) hydrogen bonds : bond 0.05188 / 3.52 ( 572) hydrogen bonds : angle 7.33332 / 5.17 ( 1518) link_ALPHA1-2 : bond 0.00680 / 0.34 ( 4) link_ALPHA1-2 : angle 1.78486 / 1.05 ( 12) link_ALPHA1-3 : bond 0.00877 / 0.48 ( 8) link_ALPHA1-3 : angle 1.34763 / 0.91 ( 24) link_ALPHA1-6 : bond 0.00629 / 0.33 ( 8) link_ALPHA1-6 : angle 1.25405 / 0.81 ( 24) link_BETA1-4 : bond 0.00492 / 0.33 ( 28) link_BETA1-4 : angle 1.96679 / 1.42 ( 84) link_BETA1-6 : bond 0.00585 / 0.29 ( 4) link_BETA1-6 : angle 1.38983 / 0.83 ( 12) link_NAG-ASN : bond 0.00277 / 0.19 ( 24) link_NAG-ASN : angle 3.01998 / 2.15 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7980 (tm-30) REVERT: E 67 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6237 (mtm110) REVERT: E 90 ASP cc_start: 0.7189 (m-30) cc_final: 0.6961 (m-30) REVERT: F 11 LEU cc_start: 0.8090 (tp) cc_final: 0.7833 (tt) REVERT: F 13 LEU cc_start: 0.8162 (mt) cc_final: 0.7322 (mt) REVERT: F 79 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7091 (mp10) REVERT: F 85 ILE cc_start: 0.8704 (mm) cc_final: 0.8455 (mm) REVERT: F 104 LYS cc_start: 0.8117 (tppt) cc_final: 0.7777 (tppt) REVERT: A 46 GLU cc_start: 0.8518 (tp30) cc_final: 0.8291 (tm-30) REVERT: A 77 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 81 MET cc_start: 0.8130 (tmm) cc_final: 0.7456 (ttp) REVERT: D 70 GLU cc_start: 0.8657 (tt0) cc_final: 0.8421 (tt0) REVERT: D 75 ILE cc_start: 0.9439 (mt) cc_final: 0.9183 (tt) REVERT: C 12 LYS cc_start: 0.8277 (mmtm) cc_final: 0.8033 (mmtm) REVERT: C 23 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8524 (tttm) REVERT: C 31 ASN cc_start: 0.8720 (t0) cc_final: 0.8477 (t0) REVERT: C 36 TRP cc_start: 0.9154 (m100) cc_final: 0.8795 (m100) REVERT: C 102 ASP cc_start: 0.9102 (p0) cc_final: 0.8725 (p0) REVERT: C 126 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8689 (m) REVERT: I 4 MET cc_start: 0.8404 (mmm) cc_final: 0.7852 (mmm) REVERT: I 11 LEU cc_start: 0.8803 (tp) cc_final: 0.8487 (tt) REVERT: I 37 GLN cc_start: 0.8518 (tt0) cc_final: 0.8212 (tt0) REVERT: I 42 GLN cc_start: 0.7461 (mt0) cc_final: 0.7135 (mt0) REVERT: I 87 TYR cc_start: 0.8705 (m-80) cc_final: 0.8406 (m-80) REVERT: I 101 GLN cc_start: 0.8656 (mm110) cc_final: 0.8442 (pm20) REVERT: I 109 ARG cc_start: 0.6416 (ptm160) cc_final: 0.5031 (pmt-80) REVERT: H 103 ASP cc_start: 0.8276 (p0) cc_final: 0.8017 (m-30) outliers start: 17 outliers final: 7 residues processed: 218 average time/residue: 0.1801 time to fit residues: 55.9973 Evaluate side-chains 187 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 178 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 173 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN A 65 GLN D 42 GLN I 6 GLN G 347 HIS G 468 HIS H 347 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 347 HIS J 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057904 restraints weight = 44027.162| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.83 r_work: 0.2793 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18993 Z= 0.222 Angle : 0.697 9.483 25929 Z= 0.356 Chirality : 0.047 0.277 3016 Planarity : 0.004 0.034 3198 Dihedral : 5.624 22.999 2466 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.24 % Allowed : 8.51 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2252 helix: -0.51 (0.85), residues: 24 sheet: -0.15 (0.16), residues: 892 loop : -0.13 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 54 TYR 0.019 0.002 TYR H 121 PHE 0.020 0.002 PHE C 64 TRP 0.019 0.002 TRP G 178 HIS 0.006 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (18875) covalent geometry : angle 0.66549 / 0.35 (25617) SS BOND : bond 0.00349 / 0.23 ( 42) SS BOND : angle 1.57489 / 1.21 ( 84) hydrogen bonds : bond 0.04738 / 3.23 ( 572) hydrogen bonds : angle 6.89484 / 4.83 ( 1518) link_ALPHA1-2 : bond 0.00445 / 0.22 ( 4) link_ALPHA1-2 : angle 2.04687 / 1.22 ( 12) link_ALPHA1-3 : bond 0.00376 / 0.19 ( 8) link_ALPHA1-3 : angle 1.63801 / 1.11 ( 24) link_ALPHA1-6 : bond 0.00347 / 0.17 ( 8) link_ALPHA1-6 : angle 1.50589 / 0.99 ( 24) link_BETA1-4 : bond 0.00466 / 0.42 ( 28) link_BETA1-4 : angle 1.85756 / 1.32 ( 84) link_BETA1-6 : bond 0.00605 / 0.29 ( 4) link_BETA1-6 : angle 2.02242 / 1.21 ( 12) link_NAG-ASN : bond 0.00303 / 0.20 ( 24) link_NAG-ASN : angle 2.70032 / 1.79 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 67 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.6277 (mtm110) REVERT: F 77 SER cc_start: 0.8540 (t) cc_final: 0.8166 (p) REVERT: F 79 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7207 (mp10) REVERT: F 104 LYS cc_start: 0.8374 (tppt) cc_final: 0.8134 (tppt) REVERT: A 12 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7777 (mmmt) REVERT: A 23 LYS cc_start: 0.9024 (tttm) cc_final: 0.8658 (tttp) REVERT: A 43 GLN cc_start: 0.8743 (mt0) cc_final: 0.8540 (mt0) REVERT: A 46 GLU cc_start: 0.8735 (tp30) cc_final: 0.8370 (tm-30) REVERT: D 18 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8283 (ttp80) REVERT: D 24 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8186 (ttm-80) REVERT: D 75 ILE cc_start: 0.9445 (mt) cc_final: 0.9214 (tt) REVERT: C 12 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8101 (mmtm) REVERT: C 23 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8452 (tttm) REVERT: C 31 ASN cc_start: 0.8770 (t0) cc_final: 0.8450 (t0) REVERT: C 65 GLN cc_start: 0.8755 (tp40) cc_final: 0.8071 (tm-30) REVERT: C 102 ASP cc_start: 0.9198 (p0) cc_final: 0.8750 (p0) REVERT: I 4 MET cc_start: 0.8374 (mmm) cc_final: 0.7870 (mmm) REVERT: I 42 GLN cc_start: 0.7641 (mt0) cc_final: 0.7334 (mt0) REVERT: I 101 GLN cc_start: 0.8650 (mm110) cc_final: 0.8413 (pm20) REVERT: I 104 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8470 (mmtt) REVERT: I 109 ARG cc_start: 0.6386 (ptm160) cc_final: 0.4927 (pmt-80) outliers start: 24 outliers final: 17 residues processed: 207 average time/residue: 0.1841 time to fit residues: 54.5735 Evaluate side-chains 187 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 146 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 HIS J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056531 restraints weight = 44176.695| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.73 r_work: 0.2762 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18993 Z= 0.298 Angle : 0.717 9.057 25929 Z= 0.363 Chirality : 0.048 0.272 3016 Planarity : 0.004 0.034 3198 Dihedral : 5.643 22.507 2466 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.29 % Allowed : 9.64 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2252 helix: -0.11 (0.87), residues: 24 sheet: -0.25 (0.15), residues: 966 loop : -0.25 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 54 TYR 0.018 0.002 TYR H 121 PHE 0.018 0.002 PHE G 410 TRP 0.020 0.002 TRP G 178 HIS 0.011 0.002 HIS H 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.30 (18875) covalent geometry : angle 0.69034 / 0.36 (25617) SS BOND : bond 0.00543 / 0.35 ( 42) SS BOND : angle 1.16539 / 0.88 ( 84) hydrogen bonds : bond 0.04838 / 3.29 ( 572) hydrogen bonds : angle 6.84189 / 4.77 ( 1518) link_ALPHA1-2 : bond 0.00280 / 0.14 ( 4) link_ALPHA1-2 : angle 2.11102 / 1.26 ( 12) link_ALPHA1-3 : bond 0.00196 / 0.09 ( 8) link_ALPHA1-3 : angle 1.89624 / 1.30 ( 24) link_ALPHA1-6 : bond 0.00317 / 0.14 ( 8) link_ALPHA1-6 : angle 1.61375 / 1.08 ( 24) link_BETA1-4 : bond 0.00317 / 0.29 ( 28) link_BETA1-4 : angle 1.89138 / 1.34 ( 84) link_BETA1-6 : bond 0.00255 / 0.12 ( 4) link_BETA1-6 : angle 1.59622 / 0.96 ( 12) link_NAG-ASN : bond 0.00541 / 0.41 ( 24) link_NAG-ASN : angle 2.59557 / 1.75 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 ARG cc_start: 0.6984 (mpp80) cc_final: 0.6723 (mpt180) REVERT: F 13 LEU cc_start: 0.8522 (mt) cc_final: 0.8253 (mt) REVERT: F 79 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7082 (mp10) REVERT: A 12 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7835 (mmmt) REVERT: A 43 GLN cc_start: 0.8805 (mt0) cc_final: 0.8588 (mt0) REVERT: A 46 GLU cc_start: 0.8821 (tp30) cc_final: 0.8447 (tm-30) REVERT: A 77 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7429 (p) REVERT: D 24 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8233 (ttm-80) REVERT: D 45 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8014 (ttp80) REVERT: C 12 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8274 (mmtt) REVERT: C 23 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8485 (tttp) REVERT: C 65 GLN cc_start: 0.8846 (tp40) cc_final: 0.7883 (tm-30) REVERT: C 94 TYR cc_start: 0.8258 (m-10) cc_final: 0.7929 (m-10) REVERT: C 102 ASP cc_start: 0.9294 (p0) cc_final: 0.8899 (p0) REVERT: I 4 MET cc_start: 0.8409 (mmm) cc_final: 0.7994 (mmm) REVERT: I 11 LEU cc_start: 0.8862 (tp) cc_final: 0.8617 (tt) REVERT: I 13 LEU cc_start: 0.8424 (mt) cc_final: 0.8213 (mm) REVERT: I 42 GLN cc_start: 0.7791 (mt0) cc_final: 0.7486 (mt0) REVERT: I 101 GLN cc_start: 0.8611 (mm110) cc_final: 0.8372 (pm20) REVERT: I 109 ARG cc_start: 0.6228 (ptm160) cc_final: 0.4759 (pmt-80) outliers start: 25 outliers final: 17 residues processed: 199 average time/residue: 0.1778 time to fit residues: 49.9986 Evaluate side-chains 181 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 468 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 193 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.080674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.058666 restraints weight = 43326.164| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.71 r_work: 0.2819 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18993 Z= 0.131 Angle : 0.621 9.233 25929 Z= 0.315 Chirality : 0.044 0.241 3016 Planarity : 0.003 0.037 3198 Dihedral : 5.200 27.063 2466 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.15 % Favored : 96.67 % Rotamer: Outliers : 1.08 % Allowed : 10.57 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2252 helix: -1.04 (0.76), residues: 28 sheet: -0.23 (0.16), residues: 960 loop : -0.08 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 18 TYR 0.015 0.001 TYR F 49 PHE 0.014 0.001 PHE H 410 TRP 0.019 0.001 TRP J 178 HIS 0.027 0.001 HIS H 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (18875) covalent geometry : angle 0.59954 / 0.31 (25617) SS BOND : bond 0.00338 / 0.28 ( 42) SS BOND : angle 1.01665 / 0.86 ( 84) hydrogen bonds : bond 0.03901 / 2.66 ( 572) hydrogen bonds : angle 6.52977 / 4.56 ( 1518) link_ALPHA1-2 : bond 0.00590 / 0.30 ( 4) link_ALPHA1-2 : angle 1.97464 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00587 / 0.31 ( 8) link_ALPHA1-3 : angle 1.38367 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00445 / 0.22 ( 8) link_ALPHA1-6 : angle 1.44553 / 0.94 ( 24) link_BETA1-4 : bond 0.00378 / 0.27 ( 28) link_BETA1-4 : angle 1.50253 / 1.08 ( 84) link_BETA1-6 : bond 0.00337 / 0.16 ( 4) link_BETA1-6 : angle 1.40057 / 0.81 ( 12) link_NAG-ASN : bond 0.00203 / 0.16 ( 24) link_NAG-ASN : angle 2.20845 / 1.52 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8246 (mp0) REVERT: E 12 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7564 (mmtt) REVERT: E 65 GLN cc_start: 0.8409 (tp-100) cc_final: 0.7925 (tm-30) REVERT: E 87 ARG cc_start: 0.6965 (mpp80) cc_final: 0.6747 (mpt180) REVERT: F 61 ARG cc_start: 0.8024 (ptm-80) cc_final: 0.7083 (ptm-80) REVERT: F 104 LYS cc_start: 0.8135 (tppt) cc_final: 0.7908 (tppt) REVERT: F 105 VAL cc_start: 0.8771 (t) cc_final: 0.8564 (t) REVERT: A 12 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7935 (mmmt) REVERT: A 46 GLU cc_start: 0.8774 (tp30) cc_final: 0.8296 (tm-30) REVERT: A 48 MET cc_start: 0.9226 (mtm) cc_final: 0.8769 (mtp) REVERT: D 45 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8033 (ttp80) REVERT: C 12 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8370 (mmtm) REVERT: C 23 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8464 (tttp) REVERT: C 65 GLN cc_start: 0.8789 (tp40) cc_final: 0.7920 (tm-30) REVERT: C 94 TYR cc_start: 0.8142 (m-10) cc_final: 0.7811 (m-10) REVERT: C 102 ASP cc_start: 0.9238 (p0) cc_final: 0.8799 (p0) REVERT: I 4 MET cc_start: 0.8352 (mmm) cc_final: 0.7939 (mmm) REVERT: I 11 LEU cc_start: 0.8828 (tp) cc_final: 0.8478 (tt) REVERT: I 42 GLN cc_start: 0.7737 (mt0) cc_final: 0.7449 (mt0) REVERT: I 54 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8186 (ttp-110) REVERT: I 101 GLN cc_start: 0.8590 (mm110) cc_final: 0.8338 (pm20) REVERT: I 109 ARG cc_start: 0.6239 (ptm160) cc_final: 0.4836 (pmt-80) REVERT: H 101 SER cc_start: 0.9444 (t) cc_final: 0.9126 (m) outliers start: 21 outliers final: 17 residues processed: 197 average time/residue: 0.1790 time to fit residues: 50.1429 Evaluate side-chains 185 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 6 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 HIS J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.078624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.056633 restraints weight = 43787.599| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.73 r_work: 0.2775 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18993 Z= 0.268 Angle : 0.679 9.483 25929 Z= 0.341 Chirality : 0.047 0.253 3016 Planarity : 0.004 0.058 3198 Dihedral : 5.358 26.077 2466 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 1.50 % Allowed : 11.04 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2252 helix: 0.12 (0.85), residues: 24 sheet: -0.29 (0.15), residues: 969 loop : -0.18 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.017 0.002 TYR F 49 PHE 0.017 0.002 PHE J 410 TRP 0.016 0.002 TRP J 178 HIS 0.009 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.27 (18875) covalent geometry : angle 0.65545 / 0.34 (25617) SS BOND : bond 0.00414 / 0.30 ( 42) SS BOND : angle 1.04993 / 0.83 ( 84) hydrogen bonds : bond 0.04492 / 3.07 ( 572) hydrogen bonds : angle 6.61581 / 4.61 ( 1518) link_ALPHA1-2 : bond 0.00301 / 0.15 ( 4) link_ALPHA1-2 : angle 2.04140 / 1.22 ( 12) link_ALPHA1-3 : bond 0.00207 / 0.09 ( 8) link_ALPHA1-3 : angle 1.83093 / 1.26 ( 24) link_ALPHA1-6 : bond 0.00321 / 0.15 ( 8) link_ALPHA1-6 : angle 1.58162 / 1.06 ( 24) link_BETA1-4 : bond 0.00248 / 0.21 ( 28) link_BETA1-4 : angle 1.72954 / 1.23 ( 84) link_BETA1-6 : bond 0.00262 / 0.13 ( 4) link_BETA1-6 : angle 1.54179 / 0.91 ( 12) link_NAG-ASN : bond 0.00410 / 0.29 ( 24) link_NAG-ASN : angle 2.32131 / 1.57 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8307 (mp0) REVERT: E 12 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7440 (mmtt) REVERT: E 65 GLN cc_start: 0.8467 (tp-100) cc_final: 0.7849 (tm-30) REVERT: E 81 MET cc_start: 0.8383 (tmm) cc_final: 0.7871 (ttt) REVERT: E 87 ARG cc_start: 0.7036 (mpp80) cc_final: 0.6767 (mpt180) REVERT: F 61 ARG cc_start: 0.7779 (ptm-80) cc_final: 0.6492 (ptm-80) REVERT: F 79 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: F 104 LYS cc_start: 0.8297 (tppt) cc_final: 0.8024 (tppt) REVERT: F 105 VAL cc_start: 0.8828 (t) cc_final: 0.8557 (t) REVERT: A 12 LYS cc_start: 0.8238 (mmtt) cc_final: 0.8004 (mmmt) REVERT: A 46 GLU cc_start: 0.8878 (tp30) cc_final: 0.8569 (tm-30) REVERT: A 48 MET cc_start: 0.9138 (mtm) cc_final: 0.8684 (mtp) REVERT: D 45 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8106 (ttp80) REVERT: C 12 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8285 (mmtm) REVERT: C 23 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8439 (tttp) REVERT: C 65 GLN cc_start: 0.8940 (tp40) cc_final: 0.7997 (tm-30) REVERT: C 94 TYR cc_start: 0.8186 (m-10) cc_final: 0.7828 (m-10) REVERT: C 102 ASP cc_start: 0.9264 (p0) cc_final: 0.8864 (p0) REVERT: I 4 MET cc_start: 0.8408 (mmm) cc_final: 0.7971 (mmm) REVERT: I 11 LEU cc_start: 0.8720 (tp) cc_final: 0.8412 (tt) REVERT: I 42 GLN cc_start: 0.7796 (mt0) cc_final: 0.7497 (mt0) REVERT: I 47 LEU cc_start: 0.9039 (tp) cc_final: 0.8741 (tt) REVERT: I 54 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8325 (ttp-110) REVERT: I 101 GLN cc_start: 0.8556 (mm110) cc_final: 0.8349 (pm20) REVERT: I 109 ARG cc_start: 0.6428 (ptm160) cc_final: 0.5059 (pmt-80) outliers start: 29 outliers final: 21 residues processed: 192 average time/residue: 0.1763 time to fit residues: 47.8749 Evaluate side-chains 186 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 162 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN C 65 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058422 restraints weight = 43590.501| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.72 r_work: 0.2804 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18993 Z= 0.148 Angle : 0.626 13.828 25929 Z= 0.312 Chirality : 0.045 0.239 3016 Planarity : 0.003 0.053 3198 Dihedral : 5.113 23.895 2466 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.40 % Rotamer: Outliers : 1.34 % Allowed : 11.55 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2252 helix: -0.83 (0.77), residues: 28 sheet: -0.19 (0.16), residues: 948 loop : -0.15 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 67 TYR 0.016 0.001 TYR F 49 PHE 0.014 0.002 PHE H 410 TRP 0.018 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (18875) covalent geometry : angle 0.60427 / 0.31 (25617) SS BOND : bond 0.00279 / 0.19 ( 42) SS BOND : angle 0.74764 / 0.60 ( 84) hydrogen bonds : bond 0.03903 / 2.66 ( 572) hydrogen bonds : angle 6.43434 / 4.48 ( 1518) link_ALPHA1-2 : bond 0.00499 / 0.25 ( 4) link_ALPHA1-2 : angle 1.96805 / 1.17 ( 12) link_ALPHA1-3 : bond 0.00470 / 0.24 ( 8) link_ALPHA1-3 : angle 1.49320 / 1.02 ( 24) link_ALPHA1-6 : bond 0.00384 / 0.18 ( 8) link_ALPHA1-6 : angle 1.47481 / 0.97 ( 24) link_BETA1-4 : bond 0.00373 / 0.31 ( 28) link_BETA1-4 : angle 1.49376 / 1.07 ( 84) link_BETA1-6 : bond 0.00252 / 0.12 ( 4) link_BETA1-6 : angle 1.49589 / 0.87 ( 12) link_NAG-ASN : bond 0.00181 / 0.13 ( 24) link_NAG-ASN : angle 2.32460 / 1.59 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8385 (mp0) REVERT: E 12 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7510 (mmtt) REVERT: E 65 GLN cc_start: 0.8475 (tp-100) cc_final: 0.7856 (tm-30) REVERT: E 87 ARG cc_start: 0.7040 (mpp80) cc_final: 0.6749 (mpt180) REVERT: F 61 ARG cc_start: 0.7788 (ptm-80) cc_final: 0.7031 (ptm-80) REVERT: F 104 LYS cc_start: 0.8282 (tppt) cc_final: 0.7992 (tppt) REVERT: F 105 VAL cc_start: 0.8855 (t) cc_final: 0.8547 (t) REVERT: A 12 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7921 (mmmt) REVERT: A 46 GLU cc_start: 0.8873 (tp30) cc_final: 0.8391 (tm-30) REVERT: A 48 MET cc_start: 0.9094 (mtm) cc_final: 0.8579 (mtp) REVERT: D 45 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8100 (ttp80) REVERT: C 12 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8311 (mmtm) REVERT: C 23 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8427 (tttp) REVERT: C 65 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8080 (tm-30) REVERT: C 94 TYR cc_start: 0.8113 (m-10) cc_final: 0.7769 (m-10) REVERT: C 102 ASP cc_start: 0.9255 (p0) cc_final: 0.8847 (p0) REVERT: I 4 MET cc_start: 0.8377 (mmm) cc_final: 0.7983 (mmm) REVERT: I 42 GLN cc_start: 0.7750 (mt0) cc_final: 0.7452 (mt0) REVERT: I 47 LEU cc_start: 0.9110 (tp) cc_final: 0.8464 (tt) REVERT: I 54 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8297 (ttp80) REVERT: I 101 GLN cc_start: 0.8557 (mm110) cc_final: 0.8343 (pm20) REVERT: I 104 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8517 (mmtt) REVERT: I 109 ARG cc_start: 0.6496 (ptm160) cc_final: 0.5265 (pmt-80) REVERT: H 101 SER cc_start: 0.9425 (t) cc_final: 0.9095 (m) outliers start: 26 outliers final: 20 residues processed: 200 average time/residue: 0.1752 time to fit residues: 49.5187 Evaluate side-chains 189 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 97 optimal weight: 0.0050 chunk 36 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059037 restraints weight = 43531.321| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.73 r_work: 0.2821 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18993 Z= 0.132 Angle : 0.625 11.359 25929 Z= 0.308 Chirality : 0.044 0.225 3016 Planarity : 0.003 0.036 3198 Dihedral : 4.967 21.779 2466 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 1.55 % Allowed : 11.86 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2252 helix: -0.76 (0.78), residues: 28 sheet: -0.15 (0.16), residues: 952 loop : -0.05 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 18 TYR 0.017 0.001 TYR F 49 PHE 0.013 0.001 PHE J 410 TRP 0.018 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18875) covalent geometry : angle 0.60368 / 0.30 (25617) SS BOND : bond 0.00234 / 0.16 ( 42) SS BOND : angle 0.71962 / 0.59 ( 84) hydrogen bonds : bond 0.03760 / 2.57 ( 572) hydrogen bonds : angle 6.33996 / 4.43 ( 1518) link_ALPHA1-2 : bond 0.00540 / 0.27 ( 4) link_ALPHA1-2 : angle 1.83910 / 1.09 ( 12) link_ALPHA1-3 : bond 0.00502 / 0.26 ( 8) link_ALPHA1-3 : angle 1.46279 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00398 / 0.20 ( 8) link_ALPHA1-6 : angle 1.45414 / 0.96 ( 24) link_BETA1-4 : bond 0.00412 / 0.34 ( 28) link_BETA1-4 : angle 1.43388 / 1.03 ( 84) link_BETA1-6 : bond 0.00251 / 0.12 ( 4) link_BETA1-6 : angle 1.48301 / 0.89 ( 12) link_NAG-ASN : bond 0.00246 / 0.21 ( 24) link_NAG-ASN : angle 2.40698 / 1.65 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8425 (mp0) REVERT: E 12 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7611 (mmtt) REVERT: E 29 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5379 (m-80) REVERT: E 65 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7782 (tm-30) REVERT: E 87 ARG cc_start: 0.7026 (mpp80) cc_final: 0.6759 (mpt180) REVERT: F 61 ARG cc_start: 0.7790 (ptm-80) cc_final: 0.7047 (ptm-80) REVERT: F 104 LYS cc_start: 0.8341 (tppt) cc_final: 0.8131 (tppt) REVERT: A 12 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8020 (mmmt) REVERT: A 46 GLU cc_start: 0.8864 (tp30) cc_final: 0.8359 (tm-30) REVERT: A 48 MET cc_start: 0.9059 (mtm) cc_final: 0.8562 (mtp) REVERT: A 111 GLU cc_start: 0.8260 (tt0) cc_final: 0.8044 (pm20) REVERT: D 24 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: D 45 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8086 (ttp80) REVERT: C 12 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8329 (mmtm) REVERT: C 23 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8455 (tttp) REVERT: C 65 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8096 (tm-30) REVERT: C 94 TYR cc_start: 0.8099 (m-10) cc_final: 0.7747 (m-10) REVERT: C 102 ASP cc_start: 0.9257 (p0) cc_final: 0.8840 (p0) REVERT: I 4 MET cc_start: 0.8365 (mmm) cc_final: 0.7974 (mmm) REVERT: I 42 GLN cc_start: 0.7744 (mt0) cc_final: 0.7461 (mt0) REVERT: I 47 LEU cc_start: 0.9107 (tp) cc_final: 0.8455 (tt) REVERT: I 54 ARG cc_start: 0.8636 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: I 101 GLN cc_start: 0.8545 (mm110) cc_final: 0.8323 (pm20) REVERT: I 104 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8476 (mmtt) REVERT: I 109 ARG cc_start: 0.6441 (ptm160) cc_final: 0.5259 (pmt-80) REVERT: H 101 SER cc_start: 0.9371 (t) cc_final: 0.9065 (m) outliers start: 30 outliers final: 23 residues processed: 201 average time/residue: 0.1736 time to fit residues: 49.6089 Evaluate side-chains 197 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 1 optimal weight: 40.0000 chunk 75 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.055872 restraints weight = 44258.110| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.80 r_work: 0.2739 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 18993 Z= 0.361 Angle : 0.759 12.138 25929 Z= 0.376 Chirality : 0.049 0.250 3016 Planarity : 0.004 0.045 3198 Dihedral : 5.466 24.004 2466 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 1.44 % Allowed : 12.33 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2252 helix: -0.43 (0.88), residues: 28 sheet: -0.28 (0.16), residues: 953 loop : -0.28 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 18 TYR 0.022 0.002 TYR I 87 PHE 0.020 0.002 PHE J 410 TRP 0.015 0.002 TRP F 35 HIS 0.008 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.36 (18875) covalent geometry : angle 0.73022 / 0.37 (25617) SS BOND : bond 0.00492 / 0.34 ( 42) SS BOND : angle 1.14463 / 0.91 ( 84) hydrogen bonds : bond 0.04872 / 3.32 ( 572) hydrogen bonds : angle 6.66338 / 4.65 ( 1518) link_ALPHA1-2 : bond 0.00175 / 0.09 ( 4) link_ALPHA1-2 : angle 2.05355 / 1.22 ( 12) link_ALPHA1-3 : bond 0.00256 / 0.15 ( 8) link_ALPHA1-3 : angle 2.11618 / 1.46 ( 24) link_ALPHA1-6 : bond 0.00350 / 0.15 ( 8) link_ALPHA1-6 : angle 1.65927 / 1.12 ( 24) link_BETA1-4 : bond 0.00389 / 0.36 ( 28) link_BETA1-4 : angle 1.83150 / 1.30 ( 84) link_BETA1-6 : bond 0.00245 / 0.12 ( 4) link_BETA1-6 : angle 1.76549 / 1.10 ( 12) link_NAG-ASN : bond 0.00604 / 0.43 ( 24) link_NAG-ASN : angle 2.95559 / 1.99 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7566 (mmtt) REVERT: E 29 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: E 65 GLN cc_start: 0.8559 (tp-100) cc_final: 0.7814 (tm-30) REVERT: E 87 ARG cc_start: 0.6999 (mpp80) cc_final: 0.6658 (mpt180) REVERT: F 61 ARG cc_start: 0.7758 (ptm-80) cc_final: 0.6729 (ptm160) REVERT: F 104 LYS cc_start: 0.8368 (tppt) cc_final: 0.8134 (tppt) REVERT: F 105 VAL cc_start: 0.8841 (t) cc_final: 0.8521 (t) REVERT: A 12 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8069 (mmmt) REVERT: A 46 GLU cc_start: 0.8924 (tp30) cc_final: 0.8401 (tm-30) REVERT: A 48 MET cc_start: 0.9166 (mtm) cc_final: 0.8764 (mtp) REVERT: A 111 GLU cc_start: 0.8375 (tt0) cc_final: 0.8119 (pm20) REVERT: D 45 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8031 (ttp80) REVERT: C 12 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8416 (mmtm) REVERT: C 23 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8381 (tttp) REVERT: C 65 GLN cc_start: 0.8930 (tp-100) cc_final: 0.7977 (tm-30) REVERT: C 94 TYR cc_start: 0.8188 (m-10) cc_final: 0.7803 (m-10) REVERT: C 102 ASP cc_start: 0.9332 (p0) cc_final: 0.8925 (p0) REVERT: I 4 MET cc_start: 0.8410 (mmm) cc_final: 0.7959 (mmm) REVERT: I 42 GLN cc_start: 0.7923 (mt0) cc_final: 0.7609 (mt0) REVERT: I 47 LEU cc_start: 0.9055 (tp) cc_final: 0.8817 (tt) REVERT: I 54 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8376 (ttp80) REVERT: I 101 GLN cc_start: 0.8563 (mm110) cc_final: 0.8331 (pm20) REVERT: I 109 ARG cc_start: 0.6315 (ptm160) cc_final: 0.5139 (pmt-80) outliers start: 28 outliers final: 24 residues processed: 191 average time/residue: 0.1839 time to fit residues: 49.5104 Evaluate side-chains 188 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059341 restraints weight = 43292.409| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.70 r_work: 0.2815 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18993 Z= 0.130 Angle : 0.654 11.279 25929 Z= 0.321 Chirality : 0.044 0.230 3016 Planarity : 0.003 0.062 3198 Dihedral : 5.067 22.100 2466 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 1.24 % Allowed : 12.58 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2252 helix: -0.81 (0.78), residues: 28 sheet: -0.09 (0.16), residues: 926 loop : -0.15 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 18 TYR 0.017 0.001 TYR F 49 PHE 0.012 0.001 PHE H 410 TRP 0.021 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (18875) covalent geometry : angle 0.63198 / 0.32 (25617) SS BOND : bond 0.00201 / 0.14 ( 42) SS BOND : angle 0.73734 / 0.61 ( 84) hydrogen bonds : bond 0.03744 / 2.55 ( 572) hydrogen bonds : angle 6.35435 / 4.43 ( 1518) link_ALPHA1-2 : bond 0.00588 / 0.30 ( 4) link_ALPHA1-2 : angle 1.94144 / 1.16 ( 12) link_ALPHA1-3 : bond 0.00575 / 0.30 ( 8) link_ALPHA1-3 : angle 1.42262 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00454 / 0.22 ( 8) link_ALPHA1-6 : angle 1.44269 / 0.94 ( 24) link_BETA1-4 : bond 0.00433 / 0.34 ( 28) link_BETA1-4 : angle 1.39257 / 0.99 ( 84) link_BETA1-6 : bond 0.00324 / 0.16 ( 4) link_BETA1-6 : angle 1.41180 / 0.82 ( 12) link_NAG-ASN : bond 0.00245 / 0.21 ( 24) link_NAG-ASN : angle 2.58488 / 1.76 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8379 (mp0) REVERT: E 12 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7662 (mmtt) REVERT: E 29 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.5381 (m-80) REVERT: E 65 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7759 (tm-30) REVERT: E 87 ARG cc_start: 0.6999 (mpp80) cc_final: 0.6717 (mpt180) REVERT: F 61 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.6882 (ptm160) REVERT: F 79 GLN cc_start: 0.7740 (mp10) cc_final: 0.7423 (mp10) REVERT: F 105 VAL cc_start: 0.8857 (t) cc_final: 0.8603 (t) REVERT: A 46 GLU cc_start: 0.8882 (tp30) cc_final: 0.8389 (tm-30) REVERT: A 81 MET cc_start: 0.8027 (tmm) cc_final: 0.7702 (tmm) REVERT: D 24 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.8039 (ttm-80) REVERT: D 45 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8044 (ttp80) REVERT: D 49 TYR cc_start: 0.8916 (p90) cc_final: 0.8641 (p90) REVERT: C 12 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8354 (mmtm) REVERT: C 23 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8399 (tttp) REVERT: C 46 GLU cc_start: 0.8748 (tp30) cc_final: 0.8299 (tt0) REVERT: C 65 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8086 (tm-30) REVERT: C 93 VAL cc_start: 0.9012 (t) cc_final: 0.8735 (p) REVERT: C 94 TYR cc_start: 0.8079 (m-10) cc_final: 0.7715 (m-10) REVERT: C 102 ASP cc_start: 0.9275 (p0) cc_final: 0.8839 (p0) REVERT: I 4 MET cc_start: 0.8345 (mmm) cc_final: 0.7966 (mmm) REVERT: I 42 GLN cc_start: 0.7774 (mt0) cc_final: 0.7500 (mt0) REVERT: I 47 LEU cc_start: 0.9117 (tp) cc_final: 0.8491 (tt) REVERT: I 54 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.8381 (ttp-110) REVERT: I 101 GLN cc_start: 0.8538 (mm110) cc_final: 0.8277 (pm20) REVERT: I 104 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8449 (mmtt) REVERT: I 109 ARG cc_start: 0.6446 (ptm160) cc_final: 0.5383 (pmt-80) outliers start: 24 outliers final: 21 residues processed: 196 average time/residue: 0.1727 time to fit residues: 48.2035 Evaluate side-chains 193 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.058791 restraints weight = 44006.872| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.83 r_work: 0.2816 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18993 Z= 0.130 Angle : 0.640 11.173 25929 Z= 0.314 Chirality : 0.044 0.220 3016 Planarity : 0.003 0.040 3198 Dihedral : 4.963 21.085 2466 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 12.33 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2252 helix: -0.62 (0.79), residues: 28 sheet: -0.06 (0.17), residues: 877 loop : -0.21 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 18 TYR 0.017 0.001 TYR F 49 PHE 0.012 0.001 PHE J 410 TRP 0.018 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18875) covalent geometry : angle 0.61860 / 0.31 (25617) SS BOND : bond 0.00217 / 0.15 ( 42) SS BOND : angle 0.69958 / 0.57 ( 84) hydrogen bonds : bond 0.03694 / 2.52 ( 572) hydrogen bonds : angle 6.24250 / 4.36 ( 1518) link_ALPHA1-2 : bond 0.00526 / 0.26 ( 4) link_ALPHA1-2 : angle 1.78719 / 1.06 ( 12) link_ALPHA1-3 : bond 0.00497 / 0.26 ( 8) link_ALPHA1-3 : angle 1.46681 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00389 / 0.18 ( 8) link_ALPHA1-6 : angle 1.44444 / 0.95 ( 24) link_BETA1-4 : bond 0.00392 / 0.32 ( 28) link_BETA1-4 : angle 1.40462 / 1.00 ( 84) link_BETA1-6 : bond 0.00282 / 0.14 ( 4) link_BETA1-6 : angle 1.40044 / 0.83 ( 12) link_NAG-ASN : bond 0.00231 / 0.20 ( 24) link_NAG-ASN : angle 2.45691 / 1.67 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4654.88 seconds wall clock time: 80 minutes 58.60 seconds (4858.60 seconds total)