Starting phenix.real_space_refine on Thu Jul 2 18:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4t_17428/07_2026/8p4t_17428.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 S 66 5.16 5 Na 1 4.78 5 C 6333 2.51 5 N 1593 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 9976 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1330 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "a" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1461 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 3, 'TRANS': 174} Chain breaks: 1 Chain: "SA" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 265 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1330 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1330 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "SB" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 265 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "SC" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 265 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "b" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1461 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 3, 'TRANS': 174} Chain breaks: 1 Chain: "c" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1461 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 3, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.05, per 1000 atoms: 0.21 Number of scatterers: 9976 At special positions: 0 Unit cell: (95.584, 96.408, 129.368, 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) S 66 16.00 Na 1 11.00 O 1983 8.00 N 1593 7.00 C 6333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS a 241 " - pdb=" SG CYS a 254 " distance=2.03 Simple disulfide: pdb=" SG CYS a 263 " - pdb=" SG CYS a 272 " distance=2.04 Simple disulfide: pdb=" SG CYS a 326 " - pdb=" SG CYS a 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 89 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS b 241 " - pdb=" SG CYS b 254 " distance=2.03 Simple disulfide: pdb=" SG CYS b 263 " - pdb=" SG CYS b 272 " distance=2.04 Simple disulfide: pdb=" SG CYS b 326 " - pdb=" SG CYS b 347 " distance=2.03 Simple disulfide: pdb=" SG CYS c 241 " - pdb=" SG CYS c 254 " distance=2.03 Simple disulfide: pdb=" SG CYS c 263 " - pdb=" SG CYS c 272 " distance=2.04 Simple disulfide: pdb=" SG CYS c 326 " - pdb=" SG CYS c 347 " distance=2.03 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 E 4 " - " MAN E 5 " " MAN H 4 " - " MAN H 5 " " MAN J 4 " - " MAN J 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " MAN E 6 " - " MAN E 7 " " BMA H 3 " - " MAN H 6 " " MAN H 6 " - " MAN H 7 " " BMA J 3 " - " MAN J 6 " " MAN J 6 " - " MAN J 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " NAG D 1 " - " FUC D 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 5 " " NAG I 1 " - " FUC I 5 " NAG-ASN " NAG A 301 " - " ASN A 73 " " NAG A 302 " - " ASN A 104 " " NAG A 303 " - " ASN A 194 " " NAG A 304 " - " ASN A 93 " " NAG B 301 " - " ASN B 73 " " NAG B 302 " - " ASN B 104 " " NAG B 303 " - " ASN B 194 " " NAG B 304 " - " ASN B 93 " " NAG C 301 " - " ASN C 73 " " NAG C 302 " - " ASN C 104 " " NAG C 303 " - " ASN C 194 " " NAG C 304 " - " ASN C 93 " " NAG D 1 " - " ASN A 112 " " NAG E 1 " - " ASN A 148 " " NAG F 1 " - " ASN a 335 " " NAG G 1 " - " ASN B 112 " " NAG H 1 " - " ASN B 148 " " NAG I 1 " - " ASN C 112 " " NAG J 1 " - " ASN C 148 " " NAG K 1 " - " ASN b 335 " " NAG L 1 " - " ASN c 335 " " NAG a 501 " - " ASN a 352 " " NAG a 502 " - " ASN a 327 " " NAG a 503 " - " ASN a 357 " " NAG b 501 " - " ASN b 352 " " NAG b 502 " - " ASN b 327 " " NAG b 503 " - " ASN b 357 " " NAG c 501 " - " ASN c 352 " " NAG c 502 " - " ASN c 327 " " NAG c 503 " - " ASN c 357 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 311.9 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 55.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.500A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 60 through 64' Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.512A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'a' and resid 256 through 262 Processing helix chain 'a' and resid 269 through 288 Processing helix chain 'a' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER a 295 " --> pdb=" O GLU a 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 307 removed outlier: 3.957A pdb=" N ILE a 306 " --> pdb=" O ARG a 302 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 322 removed outlier: 3.519A pdb=" N LEU a 312 " --> pdb=" O SER a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 357 through 360 Processing helix chain 'a' and resid 361 through 388 Processing helix chain 'a' and resid 389 through 409 removed outlier: 3.784A pdb=" N LEU a 409 " --> pdb=" O PHE a 405 " (cutoff:3.500A) Processing helix chain 'SA' and resid 3 through 8 removed outlier: 3.632A pdb=" N ILESA 8 " --> pdb=" O VALSA 4 " (cutoff:3.500A) Processing helix chain 'SA' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSA 12 " --> pdb=" O PROSA 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 9 through 12' Processing helix chain 'SA' and resid 14 through 35 Processing helix chain 'B' and resid 61 through 64 No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.512A pdb=" N PHE B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 120 through 135 removed outlier: 3.513A pdb=" N PHE C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'SB' and resid 3 through 8 removed outlier: 3.633A pdb=" N ILESB 8 " --> pdb=" O VALSB 4 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSB 12 " --> pdb=" O PROSB 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 9 through 12' Processing helix chain 'SB' and resid 14 through 35 Processing helix chain 'SC' and resid 3 through 8 removed outlier: 3.631A pdb=" N ILESC 8 " --> pdb=" O VALSC 4 " (cutoff:3.500A) Processing helix chain 'SC' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSC 12 " --> pdb=" O PROSC 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 9 through 12' Processing helix chain 'SC' and resid 14 through 35 Processing helix chain 'b' and resid 256 through 262 Processing helix chain 'b' and resid 269 through 288 Processing helix chain 'b' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER b 295 " --> pdb=" O GLU b 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE b 296 " --> pdb=" O ALA b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 302 through 307 removed outlier: 3.957A pdb=" N ILE b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 322 removed outlier: 3.518A pdb=" N LEU b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 357 through 360 Processing helix chain 'b' and resid 361 through 388 Processing helix chain 'b' and resid 389 through 409 removed outlier: 3.783A pdb=" N LEU b 409 " --> pdb=" O PHE b 405 " (cutoff:3.500A) Processing helix chain 'c' and resid 256 through 262 Processing helix chain 'c' and resid 269 through 288 Processing helix chain 'c' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER c 295 " --> pdb=" O GLU c 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE c 296 " --> pdb=" O ALA c 292 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 307 removed outlier: 3.958A pdb=" N ILE c 306 " --> pdb=" O ARG c 302 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 322 removed outlier: 3.519A pdb=" N LEU c 312 " --> pdb=" O SER c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 357 through 360 Processing helix chain 'c' and resid 361 through 388 Processing helix chain 'c' and resid 389 through 409 removed outlier: 3.784A pdb=" N LEU c 409 " --> pdb=" O PHE c 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 246 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.097A pdb=" N ARG A 183 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 246 through 248 Processing sheet with id=AA4, first strand: chain 'a' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.096A pdb=" N ARG B 183 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.097A pdb=" N ARG C 183 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'c' and resid 350 through 351 486 hydrogen bonds defined for protein. 1377 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: 1.44 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2969 1.34 - 1.46: 2498 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 10164 Sorted by residual: bond pdb=" CG1 ILE B 154 " pdb=" CD1 ILE B 154 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" CG1 ILE A 154 " pdb=" CD1 ILE A 154 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.24e+00 bond pdb=" CG1 ILE C 154 " pdb=" CD1 ILE C 154 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" CG ARG a 276 " pdb=" CD ARG a 276 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" CG ARG b 276 " pdb=" CD ARG b 276 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.68e-01 ... (remaining 10159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 13162 1.22 - 2.45: 462 2.45 - 3.67: 74 3.67 - 4.89: 18 4.89 - 6.12: 6 Bond angle restraints: 13722 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta sigma weight residual 122.38 116.26 6.12 1.81e+00 3.05e-01 1.14e+01 angle pdb=" C LEU B 126 " pdb=" N PHE B 127 " pdb=" CA PHE B 127 " ideal model delta sigma weight residual 122.38 116.27 6.11 1.81e+00 3.05e-01 1.14e+01 angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" CB PHE A 127 " ideal model delta sigma weight residual 110.44 115.59 -5.15 1.53e+00 4.27e-01 1.13e+01 angle pdb=" C LEU C 126 " pdb=" N PHE C 127 " pdb=" CA PHE C 127 " ideal model delta sigma weight residual 122.38 116.29 6.09 1.81e+00 3.05e-01 1.13e+01 angle pdb=" N PHE B 127 " pdb=" CA PHE B 127 " pdb=" CB PHE B 127 " ideal model delta sigma weight residual 110.44 115.57 -5.13 1.53e+00 4.27e-01 1.12e+01 ... (remaining 13717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.20: 6006 13.20 - 26.41: 694 26.41 - 39.61: 227 39.61 - 52.82: 24 52.82 - 66.02: 15 Dihedral angle restraints: 6966 sinusoidal: 3633 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS a 263 " pdb=" SG CYS a 263 " pdb=" SG CYS a 272 " pdb=" CB CYS a 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.79 -33.21 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS c 263 " pdb=" SG CYS c 263 " pdb=" SG CYS c 272 " pdb=" CB CYS c 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.81 -33.19 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS b 263 " pdb=" SG CYS b 263 " pdb=" SG CYS b 272 " pdb=" CB CYS b 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.83 -33.17 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 6963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1340 0.039 - 0.077: 297 0.077 - 0.116: 85 0.116 - 0.154: 33 0.154 - 0.193: 3 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA ASN a 327 " pdb=" N ASN a 327 " pdb=" C ASN a 327 " pdb=" CB ASN a 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA ASN c 327 " pdb=" N ASN c 327 " pdb=" C ASN c 327 " pdb=" CB ASN c 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA ASN b 327 " pdb=" N ASN b 327 " pdb=" C ASN b 327 " pdb=" CB ASN b 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1755 not shown) Planarity restraints: 1647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 348 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP c 348 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP c 348 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP c 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP c 348 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP c 348 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP c 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 348 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 348 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP a 348 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP a 348 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP a 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 348 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP a 348 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 348 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 348 " -0.014 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP b 348 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP b 348 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP b 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP b 348 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 348 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 348 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 348 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 348 " -0.001 2.00e-02 2.50e+03 ... (remaining 1644 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1006 2.75 - 3.29: 9769 3.29 - 3.83: 16525 3.83 - 4.36: 20122 4.36 - 4.90: 33203 Nonbonded interactions: 80625 Sorted by model distance: nonbonded pdb=" OH TYR c 333 " pdb=" O7 NAG L 1 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR a 333 " pdb=" O7 NAG F 1 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR b 333 " pdb=" O7 NAG K 1 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 79 " pdb=" OD1 ASN b 281 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU A 212 " pdb="NA NA A 305 " model vdw 2.290 3.210 ... (remaining 80620 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 'A' and resid 60 through 304) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'SA' selection = chain 'SB' selection = chain 'SC' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 1.280 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.002 0.044 10242 Z= 0.121 Angle : 0.587 7.624 13941 Z= 0.307 Chirality : 0.040 0.193 1758 Planarity : 0.003 0.024 1617 Dihedral : 11.922 66.024 4731 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.32 (0.24), residues: 1098 helix: 0.61 (0.22), residues: 498 sheet: -0.24 (0.47), residues: 105 loop : 0.08 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 276 TYR 0.015 0.001 TYR A 156 PHE 0.017 0.001 PHE a 402 TRP 0.035 0.003 TRP c 348 HIS 0.005 0.001 HIS a 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (10164) covalent geometry : angle 0.54166 / 0.30 (13722) SS BOND : bond 0.00441 / 0.25 ( 15) SS BOND : angle 1.31306 / 0.84 ( 30) hydrogen bonds : bond 0.14572 / 10.33 ( 486) hydrogen bonds : angle 6.59247 / 4.61 ( 1377) link_ALPHA1-2 : bond 0.00616 / 0.31 ( 3) link_ALPHA1-2 : angle 1.22461 / 0.74 ( 9) link_ALPHA1-3 : bond 0.00848 / 0.46 ( 6) link_ALPHA1-3 : angle 1.48549 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00647 / 0.36 ( 6) link_ALPHA1-6 : angle 1.60312 / 1.00 ( 18) link_BETA1-4 : bond 0.00351 / 0.23 ( 15) link_BETA1-4 : angle 1.51765 / 1.04 ( 45) link_BETA1-6 : bond 0.00308 / 0.15 ( 3) link_BETA1-6 : angle 1.20527 / 0.73 ( 9) link_NAG-ASN : bond 0.00240 / 0.16 ( 30) link_NAG-ASN : angle 2.36212 / 1.63 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.258 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: symmetry clash outliers start: 0 outliers final: 2 residues processed: 329 average time/residue: 0.5460 time to fit residues: 191.5090 Evaluate side-chains 198 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain c residue 366 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 281 ASN SA 17 ASN B 86 GLN SC 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084696 restraints weight = 17208.497| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.60 r_work: 0.2897 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10242 Z= 0.184 Angle : 0.644 6.037 13941 Z= 0.329 Chirality : 0.042 0.145 1758 Planarity : 0.004 0.043 1617 Dihedral : 6.674 158.405 2474 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.43 % Allowed : 12.10 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.19 (0.25), residues: 1098 helix: 1.42 (0.23), residues: 495 sheet: 0.47 (0.56), residues: 81 loop : 0.37 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 244 TYR 0.016 0.002 TYR C 156 PHE 0.029 0.002 PHE a 402 TRP 0.022 0.002 TRP b 348 HIS 0.007 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (10164) covalent geometry : angle 0.60913 / 0.32 (13722) SS BOND : bond 0.00336 / 0.23 ( 15) SS BOND : angle 0.81439 / 0.46 ( 30) hydrogen bonds : bond 0.05592 / 3.74 ( 486) hydrogen bonds : angle 5.28175 / 3.70 ( 1377) link_ALPHA1-2 : bond 0.00556 / 0.28 ( 3) link_ALPHA1-2 : angle 1.31597 / 0.79 ( 9) link_ALPHA1-3 : bond 0.00865 / 0.44 ( 6) link_ALPHA1-3 : angle 1.73393 / 1.15 ( 18) link_ALPHA1-6 : bond 0.00574 / 0.33 ( 6) link_ALPHA1-6 : angle 1.62115 / 1.01 ( 18) link_BETA1-4 : bond 0.00378 / 0.26 ( 15) link_BETA1-4 : angle 1.59947 / 1.11 ( 45) link_BETA1-6 : bond 0.00134 / 0.06 ( 3) link_BETA1-6 : angle 1.39390 / 0.84 ( 9) link_NAG-ASN : bond 0.00317 / 0.15 ( 30) link_NAG-ASN : angle 2.17258 / 1.50 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7886 (t0) cc_final: 0.7655 (t0) REVERT: A 182 ASP cc_start: 0.8955 (t0) cc_final: 0.8510 (t0) REVERT: A 218 ARG cc_start: 0.8825 (mtp85) cc_final: 0.8039 (mtp85) REVERT: B 120 ASP cc_start: 0.7921 (t0) cc_final: 0.7687 (t0) REVERT: B 183 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7094 (mmp80) REVERT: B 196 THR cc_start: 0.8652 (m) cc_final: 0.8278 (p) REVERT: B 218 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8507 (mtm180) REVERT: B 219 LYS cc_start: 0.8626 (tptp) cc_final: 0.8317 (tptp) REVERT: C 120 ASP cc_start: 0.7894 (t0) cc_final: 0.7661 (t0) REVERT: C 144 LYS cc_start: 0.8075 (mttt) cc_final: 0.7612 (mtpm) REVERT: C 155 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7786 (mt-10) REVERT: C 168 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: C 182 ASP cc_start: 0.9127 (t0) cc_final: 0.8740 (t0) outliers start: 36 outliers final: 16 residues processed: 234 average time/residue: 0.5111 time to fit residues: 128.0641 Evaluate side-chains 208 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 0.0030 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 304 ASN ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN c 264 ASN c 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085730 restraints weight = 17153.983| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.58 r_work: 0.2908 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10242 Z= 0.130 Angle : 0.600 7.315 13941 Z= 0.302 Chirality : 0.040 0.144 1758 Planarity : 0.004 0.040 1617 Dihedral : 5.615 52.396 2469 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.81 % Allowed : 14.29 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.30 (0.25), residues: 1098 helix: 1.46 (0.23), residues: 513 sheet: 0.48 (0.44), residues: 105 loop : 0.46 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 183 TYR 0.011 0.001 TYR C 156 PHE 0.022 0.001 PHE b 402 TRP 0.012 0.001 TRP b 348 HIS 0.005 0.000 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10164) covalent geometry : angle 0.56469 / 0.30 (13722) SS BOND : bond 0.00448 / 0.35 ( 15) SS BOND : angle 1.14645 / 0.58 ( 30) hydrogen bonds : bond 0.04721 / 3.17 ( 486) hydrogen bonds : angle 4.92099 / 3.45 ( 1377) link_ALPHA1-2 : bond 0.00679 / 0.34 ( 3) link_ALPHA1-2 : angle 1.22468 / 0.73 ( 9) link_ALPHA1-3 : bond 0.00823 / 0.43 ( 6) link_ALPHA1-3 : angle 1.54795 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00609 / 0.34 ( 6) link_ALPHA1-6 : angle 1.62837 / 1.00 ( 18) link_BETA1-4 : bond 0.00386 / 0.24 ( 15) link_BETA1-4 : angle 1.49980 / 1.04 ( 45) link_BETA1-6 : bond 0.00114 / 0.06 ( 3) link_BETA1-6 : angle 1.38118 / 0.83 ( 9) link_NAG-ASN : bond 0.00281 / 0.13 ( 30) link_NAG-ASN : angle 2.03737 / 1.42 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.255 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: A 120 ASP cc_start: 0.7809 (t0) cc_final: 0.7499 (t0) REVERT: A 218 ARG cc_start: 0.8826 (mtp85) cc_final: 0.8599 (mtp85) REVERT: B 120 ASP cc_start: 0.7906 (t0) cc_final: 0.7566 (t0) REVERT: B 144 LYS cc_start: 0.8257 (mtpt) cc_final: 0.8053 (mtpp) REVERT: B 196 THR cc_start: 0.8722 (m) cc_final: 0.8385 (p) REVERT: C 120 ASP cc_start: 0.7893 (t0) cc_final: 0.7549 (t0) REVERT: C 155 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 168 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: C 182 ASP cc_start: 0.9131 (t0) cc_final: 0.8664 (t0) REVERT: C 219 LYS cc_start: 0.8549 (tptp) cc_final: 0.8336 (tptp) REVERT: c 375 GLU cc_start: 0.7088 (tt0) cc_final: 0.6817 (tm-30) outliers start: 40 outliers final: 17 residues processed: 219 average time/residue: 0.5378 time to fit residues: 126.6170 Evaluate side-chains 206 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 35 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 GLN c 264 ASN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.082430 restraints weight = 17270.898| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.63 r_work: 0.2886 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10242 Z= 0.149 Angle : 0.605 8.257 13941 Z= 0.303 Chirality : 0.040 0.147 1758 Planarity : 0.004 0.058 1617 Dihedral : 5.619 53.644 2469 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.05 % Allowed : 15.43 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.41 (0.26), residues: 1098 helix: 1.48 (0.23), residues: 531 sheet: 0.85 (0.47), residues: 105 loop : 0.47 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 183 TYR 0.013 0.001 TYR C 151 PHE 0.020 0.001 PHE b 402 TRP 0.014 0.001 TRP b 348 HIS 0.005 0.000 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (10164) covalent geometry : angle 0.56737 / 0.30 (13722) SS BOND : bond 0.00430 / 0.30 ( 15) SS BOND : angle 1.39644 / 0.66 ( 30) hydrogen bonds : bond 0.04643 / 3.11 ( 486) hydrogen bonds : angle 4.77107 / 3.36 ( 1377) link_ALPHA1-2 : bond 0.00586 / 0.29 ( 3) link_ALPHA1-2 : angle 1.26356 / 0.76 ( 9) link_ALPHA1-3 : bond 0.00713 / 0.38 ( 6) link_ALPHA1-3 : angle 1.56339 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00570 / 0.32 ( 6) link_ALPHA1-6 : angle 1.61220 / 1.00 ( 18) link_BETA1-4 : bond 0.00343 / 0.21 ( 15) link_BETA1-4 : angle 1.53973 / 1.07 ( 45) link_BETA1-6 : bond 0.00087 / 0.04 ( 3) link_BETA1-6 : angle 1.40840 / 0.85 ( 9) link_NAG-ASN : bond 0.00259 / 0.12 ( 30) link_NAG-ASN : angle 2.08520 / 1.47 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7966 (t0) cc_final: 0.7640 (t0) REVERT: A 155 GLU cc_start: 0.8611 (tt0) cc_final: 0.8288 (tt0) REVERT: B 120 ASP cc_start: 0.7945 (t0) cc_final: 0.7568 (t0) REVERT: B 196 THR cc_start: 0.8859 (m) cc_final: 0.8482 (p) REVERT: B 218 ARG cc_start: 0.8837 (mtp85) cc_final: 0.8534 (mtp85) REVERT: B 219 LYS cc_start: 0.8618 (tptp) cc_final: 0.8355 (tptp) REVERT: C 120 ASP cc_start: 0.8001 (t0) cc_final: 0.7588 (t0) REVERT: C 155 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 168 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: C 182 ASP cc_start: 0.9090 (t0) cc_final: 0.8623 (t0) REVERT: SB 25 MET cc_start: 0.8221 (mmm) cc_final: 0.7941 (mmm) REVERT: b 256 ASP cc_start: 0.6855 (p0) cc_final: 0.6618 (p0) outliers start: 32 outliers final: 24 residues processed: 217 average time/residue: 0.5400 time to fit residues: 125.4848 Evaluate side-chains 204 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 364 ASP Chi-restraints excluded: chain SA residue 35 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 260 ILE Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 304 ASN B 86 GLN b 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085531 restraints weight = 17194.382| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.56 r_work: 0.2886 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10242 Z= 0.114 Angle : 0.577 9.078 13941 Z= 0.289 Chirality : 0.039 0.157 1758 Planarity : 0.003 0.031 1617 Dihedral : 5.529 53.700 2469 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.52 % Allowed : 16.57 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.58 (0.26), residues: 1098 helix: 1.63 (0.23), residues: 531 sheet: 1.14 (0.48), residues: 105 loop : 0.48 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 183 TYR 0.012 0.001 TYR C 156 PHE 0.016 0.001 PHE b 402 TRP 0.007 0.001 TRP b 348 HIS 0.001 0.000 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (10164) covalent geometry : angle 0.54199 / 0.28 (13722) SS BOND : bond 0.00296 / 0.22 ( 15) SS BOND : angle 1.00006 / 0.54 ( 30) hydrogen bonds : bond 0.04254 / 2.84 ( 486) hydrogen bonds : angle 4.61618 / 3.24 ( 1377) link_ALPHA1-2 : bond 0.00633 / 0.32 ( 3) link_ALPHA1-2 : angle 1.23575 / 0.74 ( 9) link_ALPHA1-3 : bond 0.00823 / 0.43 ( 6) link_ALPHA1-3 : angle 1.47722 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00604 / 0.34 ( 6) link_ALPHA1-6 : angle 1.60626 / 0.99 ( 18) link_BETA1-4 : bond 0.00374 / 0.24 ( 15) link_BETA1-4 : angle 1.44102 / 1.00 ( 45) link_BETA1-6 : bond 0.00188 / 0.09 ( 3) link_BETA1-6 : angle 1.32248 / 0.79 ( 9) link_NAG-ASN : bond 0.00190 / 0.12 ( 30) link_NAG-ASN : angle 2.01193 / 1.43 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7924 (t0) cc_final: 0.7623 (t0) REVERT: A 155 GLU cc_start: 0.8596 (tt0) cc_final: 0.8279 (tt0) REVERT: A 168 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: B 120 ASP cc_start: 0.7959 (t0) cc_final: 0.7568 (t0) REVERT: B 144 LYS cc_start: 0.8418 (mmmm) cc_final: 0.7467 (mmmm) REVERT: B 182 ASP cc_start: 0.8923 (m-30) cc_final: 0.8629 (m-30) REVERT: B 196 THR cc_start: 0.8843 (m) cc_final: 0.8459 (p) REVERT: B 213 THR cc_start: 0.9057 (m) cc_final: 0.8834 (p) REVERT: B 217 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9070 (m) REVERT: B 219 LYS cc_start: 0.8608 (tptp) cc_final: 0.8307 (tptp) REVERT: C 120 ASP cc_start: 0.8007 (t0) cc_final: 0.7620 (t0) REVERT: C 155 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7787 (mt-10) REVERT: C 168 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: SB 25 MET cc_start: 0.8208 (mmm) cc_final: 0.7924 (mmm) REVERT: c 364 ASP cc_start: 0.8895 (m-30) cc_final: 0.8654 (t0) outliers start: 37 outliers final: 21 residues processed: 225 average time/residue: 0.5232 time to fit residues: 126.6568 Evaluate side-chains 214 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 260 ILE Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 304 ASN B 86 GLN b 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.121930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082156 restraints weight = 17384.152| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.61 r_work: 0.2831 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10242 Z= 0.158 Angle : 0.616 10.791 13941 Z= 0.304 Chirality : 0.040 0.152 1758 Planarity : 0.004 0.033 1617 Dihedral : 5.571 55.512 2469 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.71 % Allowed : 17.62 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.37 (0.26), residues: 1098 helix: 1.56 (0.23), residues: 531 sheet: 0.49 (0.46), residues: 123 loop : 0.37 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 183 TYR 0.012 0.001 TYR C 156 PHE 0.012 0.001 PHE b 402 TRP 0.013 0.001 TRP b 348 HIS 0.002 0.000 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10164) covalent geometry : angle 0.58045 / 0.30 (13722) SS BOND : bond 0.00382 / 0.26 ( 15) SS BOND : angle 1.20135 / 0.67 ( 30) hydrogen bonds : bond 0.04465 / 3.00 ( 486) hydrogen bonds : angle 4.69685 / 3.31 ( 1377) link_ALPHA1-2 : bond 0.00559 / 0.28 ( 3) link_ALPHA1-2 : angle 1.30188 / 0.78 ( 9) link_ALPHA1-3 : bond 0.00716 / 0.38 ( 6) link_ALPHA1-3 : angle 1.56401 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00553 / 0.31 ( 6) link_ALPHA1-6 : angle 1.57810 / 0.98 ( 18) link_BETA1-4 : bond 0.00339 / 0.22 ( 15) link_BETA1-4 : angle 1.50644 / 1.03 ( 45) link_BETA1-6 : bond 0.00048 / 0.02 ( 3) link_BETA1-6 : angle 1.43122 / 0.86 ( 9) link_NAG-ASN : bond 0.00225 / 0.13 ( 30) link_NAG-ASN : angle 2.09009 / 1.48 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8066 (t0) cc_final: 0.7725 (t0) REVERT: A 155 GLU cc_start: 0.8618 (tt0) cc_final: 0.8348 (tt0) REVERT: A 168 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: A 217 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8960 (m) REVERT: a 281 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8821 (t0) REVERT: B 74 MET cc_start: 0.9158 (mmt) cc_final: 0.8886 (mmt) REVERT: B 120 ASP cc_start: 0.8060 (t0) cc_final: 0.7633 (t0) REVERT: B 144 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7402 (mmmm) REVERT: B 182 ASP cc_start: 0.8972 (m-30) cc_final: 0.8472 (t0) REVERT: B 196 THR cc_start: 0.8924 (m) cc_final: 0.8563 (p) REVERT: B 217 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9029 (m) REVERT: B 219 LYS cc_start: 0.8635 (tptp) cc_final: 0.8348 (tptp) REVERT: C 120 ASP cc_start: 0.8127 (t0) cc_final: 0.7703 (t0) REVERT: C 155 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 159 THR cc_start: 0.8335 (t) cc_final: 0.8081 (p) REVERT: C 168 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: SB 25 MET cc_start: 0.8254 (mmm) cc_final: 0.7977 (mmm) outliers start: 39 outliers final: 21 residues processed: 213 average time/residue: 0.5533 time to fit residues: 126.5152 Evaluate side-chains 201 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 281 ASN Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080619 restraints weight = 17355.154| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.68 r_work: 0.2821 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10242 Z= 0.159 Angle : 0.623 10.720 13941 Z= 0.309 Chirality : 0.040 0.172 1758 Planarity : 0.004 0.034 1617 Dihedral : 5.572 55.159 2469 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.62 % Allowed : 18.29 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.37 (0.26), residues: 1098 helix: 1.60 (0.23), residues: 531 sheet: 0.50 (0.46), residues: 123 loop : 0.30 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 183 TYR 0.012 0.001 TYR C 156 PHE 0.014 0.001 PHE a 361 TRP 0.011 0.001 TRP b 348 HIS 0.003 0.000 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10164) covalent geometry : angle 0.58921 / 0.30 (13722) SS BOND : bond 0.00345 / 0.24 ( 15) SS BOND : angle 1.17489 / 0.65 ( 30) hydrogen bonds : bond 0.04461 / 2.98 ( 486) hydrogen bonds : angle 4.66986 / 3.30 ( 1377) link_ALPHA1-2 : bond 0.00563 / 0.28 ( 3) link_ALPHA1-2 : angle 1.29090 / 0.77 ( 9) link_ALPHA1-3 : bond 0.00756 / 0.40 ( 6) link_ALPHA1-3 : angle 1.54782 / 1.01 ( 18) link_ALPHA1-6 : bond 0.00562 / 0.31 ( 6) link_ALPHA1-6 : angle 1.56476 / 0.97 ( 18) link_BETA1-4 : bond 0.00351 / 0.23 ( 15) link_BETA1-4 : angle 1.45937 / 1.00 ( 45) link_BETA1-6 : bond 0.00037 / 0.02 ( 3) link_BETA1-6 : angle 1.44795 / 0.87 ( 9) link_NAG-ASN : bond 0.00195 / 0.12 ( 30) link_NAG-ASN : angle 2.09290 / 1.49 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8162 (t0) cc_final: 0.7799 (t0) REVERT: A 159 THR cc_start: 0.8489 (t) cc_final: 0.8213 (p) REVERT: A 168 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: A 217 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8933 (m) REVERT: A 218 ARG cc_start: 0.8852 (mtp85) cc_final: 0.8572 (mtp85) REVERT: a 281 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8775 (t0) REVERT: B 74 MET cc_start: 0.9065 (mmt) cc_final: 0.8789 (mmt) REVERT: B 120 ASP cc_start: 0.8126 (t0) cc_final: 0.7668 (t0) REVERT: B 182 ASP cc_start: 0.8969 (m-30) cc_final: 0.8541 (t0) REVERT: B 196 THR cc_start: 0.8965 (m) cc_final: 0.8631 (p) REVERT: B 218 ARG cc_start: 0.8750 (mtm180) cc_final: 0.8449 (mtp-110) REVERT: C 120 ASP cc_start: 0.8204 (t0) cc_final: 0.7746 (t0) REVERT: C 155 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 159 THR cc_start: 0.8400 (t) cc_final: 0.8155 (p) REVERT: C 168 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: C 219 LYS cc_start: 0.8603 (tptp) cc_final: 0.8329 (tptp) REVERT: SB 25 MET cc_start: 0.8324 (mmm) cc_final: 0.8032 (mmm) outliers start: 38 outliers final: 24 residues processed: 211 average time/residue: 0.5535 time to fit residues: 125.0473 Evaluate side-chains 211 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 281 ASN Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain a residue 364 ASP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082517 restraints weight = 17138.206| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.51 r_work: 0.2854 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10242 Z= 0.135 Angle : 0.631 11.924 13941 Z= 0.309 Chirality : 0.039 0.180 1758 Planarity : 0.004 0.036 1617 Dihedral : 5.532 55.191 2469 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.05 % Allowed : 19.81 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.42 (0.26), residues: 1098 helix: 1.66 (0.23), residues: 531 sheet: 0.60 (0.46), residues: 123 loop : 0.30 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 244 TYR 0.012 0.001 TYR b 403 PHE 0.009 0.001 PHE c 361 TRP 0.008 0.001 TRP b 348 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10164) covalent geometry : angle 0.59974 / 0.30 (13722) SS BOND : bond 0.00314 / 0.22 ( 15) SS BOND : angle 1.07761 / 0.61 ( 30) hydrogen bonds : bond 0.04346 / 2.90 ( 486) hydrogen bonds : angle 4.59791 / 3.24 ( 1377) link_ALPHA1-2 : bond 0.00579 / 0.29 ( 3) link_ALPHA1-2 : angle 1.28404 / 0.77 ( 9) link_ALPHA1-3 : bond 0.00759 / 0.40 ( 6) link_ALPHA1-3 : angle 1.50139 / 0.98 ( 18) link_ALPHA1-6 : bond 0.00576 / 0.32 ( 6) link_ALPHA1-6 : angle 1.55271 / 0.97 ( 18) link_BETA1-4 : bond 0.00354 / 0.23 ( 15) link_BETA1-4 : angle 1.43177 / 0.98 ( 45) link_BETA1-6 : bond 0.00080 / 0.04 ( 3) link_BETA1-6 : angle 1.38107 / 0.83 ( 9) link_NAG-ASN : bond 0.00138 / 0.08 ( 30) link_NAG-ASN : angle 2.04179 / 1.45 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.403 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: A 120 ASP cc_start: 0.8286 (t0) cc_final: 0.8084 (t0) REVERT: A 155 GLU cc_start: 0.8651 (tt0) cc_final: 0.8381 (tt0) REVERT: A 168 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: a 281 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8921 (t0) REVERT: B 74 MET cc_start: 0.9135 (mmt) cc_final: 0.8859 (mmt) REVERT: B 120 ASP cc_start: 0.8260 (t0) cc_final: 0.7857 (t0) REVERT: B 182 ASP cc_start: 0.8960 (m-30) cc_final: 0.8531 (t0) REVERT: B 196 THR cc_start: 0.9066 (m) cc_final: 0.8779 (p) REVERT: B 218 ARG cc_start: 0.8855 (mtm180) cc_final: 0.8569 (mtp-110) REVERT: C 120 ASP cc_start: 0.8399 (t0) cc_final: 0.7979 (t0) REVERT: C 144 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7496 (mtpp) REVERT: C 155 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 159 THR cc_start: 0.8537 (t) cc_final: 0.8292 (p) REVERT: C 160 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8702 (mttp) REVERT: C 219 LYS cc_start: 0.8664 (tptp) cc_final: 0.8404 (tptp) REVERT: SB 25 MET cc_start: 0.8336 (mmm) cc_final: 0.8048 (mmm) outliers start: 32 outliers final: 23 residues processed: 213 average time/residue: 0.5667 time to fit residues: 129.4219 Evaluate side-chains 208 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 281 ASN Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 77 optimal weight: 7.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082173 restraints weight = 17395.651| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.59 r_work: 0.2858 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10242 Z= 0.132 Angle : 0.627 12.677 13941 Z= 0.309 Chirality : 0.039 0.200 1758 Planarity : 0.004 0.037 1617 Dihedral : 5.487 55.183 2469 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.95 % Allowed : 21.24 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.47 (0.26), residues: 1098 helix: 1.74 (0.23), residues: 528 sheet: 0.70 (0.47), residues: 123 loop : 0.23 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 121 TYR 0.012 0.001 TYR C 156 PHE 0.008 0.001 PHE c 361 TRP 0.007 0.001 TRP b 348 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10164) covalent geometry : angle 0.59761 / 0.30 (13722) SS BOND : bond 0.00318 / 0.22 ( 15) SS BOND : angle 1.08201 / 0.60 ( 30) hydrogen bonds : bond 0.04269 / 2.85 ( 486) hydrogen bonds : angle 4.59066 / 3.23 ( 1377) link_ALPHA1-2 : bond 0.00566 / 0.28 ( 3) link_ALPHA1-2 : angle 1.29127 / 0.77 ( 9) link_ALPHA1-3 : bond 0.00745 / 0.39 ( 6) link_ALPHA1-3 : angle 1.48706 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00569 / 0.31 ( 6) link_ALPHA1-6 : angle 1.54021 / 0.96 ( 18) link_BETA1-4 : bond 0.00351 / 0.22 ( 15) link_BETA1-4 : angle 1.42691 / 0.98 ( 45) link_BETA1-6 : bond 0.00104 / 0.05 ( 3) link_BETA1-6 : angle 1.38399 / 0.83 ( 9) link_NAG-ASN : bond 0.00128 / 0.08 ( 30) link_NAG-ASN : angle 1.94399 / 1.37 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.8078 (tpp80) REVERT: A 168 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: a 281 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8927 (t0) REVERT: B 74 MET cc_start: 0.9139 (mmt) cc_final: 0.8866 (mmt) REVERT: B 120 ASP cc_start: 0.8300 (t0) cc_final: 0.7922 (t0) REVERT: B 182 ASP cc_start: 0.8960 (m-30) cc_final: 0.8484 (t0) REVERT: B 196 THR cc_start: 0.9093 (m) cc_final: 0.8822 (p) REVERT: B 218 ARG cc_start: 0.8840 (mtm180) cc_final: 0.8568 (mtp-110) REVERT: C 120 ASP cc_start: 0.8430 (t0) cc_final: 0.8009 (t0) REVERT: C 144 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7659 (mtpp) REVERT: C 155 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 159 THR cc_start: 0.8568 (t) cc_final: 0.8319 (p) REVERT: C 160 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8708 (mttp) REVERT: C 219 LYS cc_start: 0.8682 (tptp) cc_final: 0.8418 (tptp) REVERT: SB 25 MET cc_start: 0.8330 (mmm) cc_final: 0.8054 (mmm) REVERT: c 364 ASP cc_start: 0.8921 (m-30) cc_final: 0.8540 (t0) outliers start: 31 outliers final: 25 residues processed: 206 average time/residue: 0.5957 time to fit residues: 131.3217 Evaluate side-chains 206 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 281 ASN Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 255 PHE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Chi-restraints excluded: chain c residue 255 PHE Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080891 restraints weight = 17444.347| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.58 r_work: 0.2828 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10242 Z= 0.171 Angle : 0.673 13.815 13941 Z= 0.328 Chirality : 0.040 0.215 1758 Planarity : 0.004 0.037 1617 Dihedral : 5.529 55.479 2469 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.67 % Allowed : 21.62 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.47 (0.26), residues: 1098 helix: 1.75 (0.23), residues: 525 sheet: 0.71 (0.47), residues: 123 loop : 0.23 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 183 TYR 0.012 0.001 TYR C 156 PHE 0.011 0.001 PHE a 361 TRP 0.010 0.001 TRP b 348 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (10164) covalent geometry : angle 0.64117 / 0.32 (13722) SS BOND : bond 0.00382 / 0.25 ( 15) SS BOND : angle 1.47079 / 0.76 ( 30) hydrogen bonds : bond 0.04402 / 2.94 ( 486) hydrogen bonds : angle 4.66307 / 3.29 ( 1377) link_ALPHA1-2 : bond 0.00572 / 0.29 ( 3) link_ALPHA1-2 : angle 1.32418 / 0.80 ( 9) link_ALPHA1-3 : bond 0.00712 / 0.38 ( 6) link_ALPHA1-3 : angle 1.52861 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00540 / 0.30 ( 6) link_ALPHA1-6 : angle 1.52998 / 0.96 ( 18) link_BETA1-4 : bond 0.00353 / 0.22 ( 15) link_BETA1-4 : angle 1.44786 / 0.99 ( 45) link_BETA1-6 : bond 0.00056 / 0.03 ( 3) link_BETA1-6 : angle 1.43725 / 0.86 ( 9) link_NAG-ASN : bond 0.00238 / 0.14 ( 30) link_NAG-ASN : angle 2.08281 / 1.47 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8107 (tpp80) REVERT: A 168 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: A 218 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8315 (mtt-85) REVERT: a 281 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8990 (t0) REVERT: B 74 MET cc_start: 0.9137 (mmt) cc_final: 0.8864 (mmt) REVERT: B 120 ASP cc_start: 0.8379 (t0) cc_final: 0.7965 (t0) REVERT: B 121 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7871 (tpp80) REVERT: B 144 LYS cc_start: 0.8484 (mmmm) cc_final: 0.7683 (mmmm) REVERT: B 182 ASP cc_start: 0.8993 (m-30) cc_final: 0.8552 (t0) REVERT: B 196 THR cc_start: 0.9117 (m) cc_final: 0.8877 (p) REVERT: B 219 LYS cc_start: 0.8557 (tptp) cc_final: 0.8275 (tptp) REVERT: C 120 ASP cc_start: 0.8488 (t0) cc_final: 0.8055 (t0) REVERT: C 144 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7667 (mtpp) REVERT: C 155 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7906 (mt-10) REVERT: C 159 THR cc_start: 0.8587 (t) cc_final: 0.8347 (p) REVERT: C 160 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8746 (mttp) REVERT: C 219 LYS cc_start: 0.8699 (tptp) cc_final: 0.8442 (tptp) REVERT: SB 25 MET cc_start: 0.8368 (mmm) cc_final: 0.8094 (mmm) REVERT: b 268 ASP cc_start: 0.8682 (t70) cc_final: 0.8339 (t0) REVERT: c 268 ASP cc_start: 0.8629 (t70) cc_final: 0.8299 (t0) REVERT: c 364 ASP cc_start: 0.8955 (m-30) cc_final: 0.8535 (t0) outliers start: 28 outliers final: 25 residues processed: 201 average time/residue: 0.6029 time to fit residues: 129.7215 Evaluate side-chains 208 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 281 ASN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 255 PHE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Chi-restraints excluded: chain c residue 255 PHE Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.120485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081985 restraints weight = 17316.390| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.53 r_work: 0.2849 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10242 Z= 0.138 Angle : 0.653 13.632 13941 Z= 0.320 Chirality : 0.040 0.204 1758 Planarity : 0.004 0.039 1617 Dihedral : 5.492 55.174 2469 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.14 % Allowed : 21.71 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.39 (0.26), residues: 1098 helix: 1.77 (0.23), residues: 525 sheet: 0.26 (0.46), residues: 132 loop : 0.22 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 183 TYR 0.012 0.001 TYR C 156 PHE 0.008 0.001 PHE C 99 TRP 0.007 0.001 TRP b 348 HIS 0.003 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10164) covalent geometry : angle 0.62289 / 0.31 (13722) SS BOND : bond 0.00316 / 0.22 ( 15) SS BOND : angle 1.43677 / 0.74 ( 30) hydrogen bonds : bond 0.04296 / 2.86 ( 486) hydrogen bonds : angle 4.63287 / 3.27 ( 1377) link_ALPHA1-2 : bond 0.00555 / 0.28 ( 3) link_ALPHA1-2 : angle 1.30133 / 0.78 ( 9) link_ALPHA1-3 : bond 0.00733 / 0.39 ( 6) link_ALPHA1-3 : angle 1.48138 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00567 / 0.31 ( 6) link_ALPHA1-6 : angle 1.52598 / 0.95 ( 18) link_BETA1-4 : bond 0.00365 / 0.23 ( 15) link_BETA1-4 : angle 1.42382 / 0.98 ( 45) link_BETA1-6 : bond 0.00092 / 0.05 ( 3) link_BETA1-6 : angle 1.38714 / 0.83 ( 9) link_NAG-ASN : bond 0.00153 / 0.09 ( 30) link_NAG-ASN : angle 2.00114 / 1.41 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3445.48 seconds wall clock time: 59 minutes 40.60 seconds (3580.60 seconds total)