Starting phenix.real_space_refine on Wed Feb 4 08:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4t_17428/02_2026/8p4t_17428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4t_17428/02_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_17428/02_2026/8p4t_17428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_2026/8p4t_17428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_2026/8p4t_17428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_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-2.0-5952/lib/python3.9/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, 57 Unusual residues: {' NA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2.63, per 1000 atoms: 0.26 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: 1.08 Conformation dependent library (CDL) restraints added in 386.4 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: 0.32 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: 1.57 Time building geometry restraints manager: 1.31 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 2.470 ... (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: 1.450 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.300 Find NCS groups from input model: 0.210 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:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 covalent geometry : bond 0.00240 (10164) covalent geometry : angle 0.54166 (13722) SS BOND : bond 0.00441 ( 15) SS BOND : angle 1.31306 ( 30) hydrogen bonds : bond 0.14572 ( 486) hydrogen bonds : angle 6.59247 ( 1377) link_ALPHA1-2 : bond 0.00616 ( 3) link_ALPHA1-2 : angle 1.22461 ( 9) link_ALPHA1-3 : bond 0.00848 ( 6) link_ALPHA1-3 : angle 1.48549 ( 18) link_ALPHA1-6 : bond 0.00647 ( 6) link_ALPHA1-6 : angle 1.60312 ( 18) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.51765 ( 45) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 1.20527 ( 9) link_NAG-ASN : bond 0.00240 ( 30) link_NAG-ASN : angle 2.36212 ( 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 : 0.301 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: 0.6028 time to fit residues: 210.9337 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 : 0.445 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 281 ASN B 86 GLN SC 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083479 restraints weight = 17226.891| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.60 r_work: 0.2866 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10242 Z= 0.208 Angle : 0.659 6.291 13941 Z= 0.336 Chirality : 0.043 0.145 1758 Planarity : 0.004 0.048 1617 Dihedral : 6.727 158.380 2474 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.62 % Allowed : 12.29 % Favored : 84.10 % 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: 1.00 (0.25), residues: 1098 helix: 1.22 (0.23), residues: 510 sheet: 0.54 (0.55), residues: 81 loop : 0.25 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 244 TYR 0.017 0.002 TYR C 156 PHE 0.030 0.002 PHE a 402 TRP 0.024 0.002 TRP b 348 HIS 0.007 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00473 (10164) covalent geometry : angle 0.62342 (13722) SS BOND : bond 0.00522 ( 15) SS BOND : angle 0.84481 ( 30) hydrogen bonds : bond 0.05660 ( 486) hydrogen bonds : angle 5.28552 ( 1377) link_ALPHA1-2 : bond 0.00580 ( 3) link_ALPHA1-2 : angle 1.36907 ( 9) link_ALPHA1-3 : bond 0.00741 ( 6) link_ALPHA1-3 : angle 1.72941 ( 18) link_ALPHA1-6 : bond 0.00556 ( 6) link_ALPHA1-6 : angle 1.62116 ( 18) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.65388 ( 45) link_BETA1-6 : bond 0.00119 ( 3) link_BETA1-6 : angle 1.44707 ( 9) link_NAG-ASN : bond 0.00401 ( 30) link_NAG-ASN : angle 2.21142 ( 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 261 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.287 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: 0.7923 (t0) cc_final: 0.7676 (t0) REVERT: A 182 ASP cc_start: 0.8995 (t0) cc_final: 0.8530 (t0) REVERT: A 218 ARG cc_start: 0.8844 (mtp85) cc_final: 0.8563 (mtp85) REVERT: B 120 ASP cc_start: 0.7974 (t0) cc_final: 0.7742 (t0) REVERT: B 183 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7110 (mmp80) REVERT: B 196 THR cc_start: 0.8735 (m) cc_final: 0.8391 (p) REVERT: C 120 ASP cc_start: 0.7994 (t0) cc_final: 0.7754 (t0) REVERT: C 144 LYS cc_start: 0.8075 (mttt) cc_final: 0.7602 (mtpm) REVERT: C 155 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 168 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: C 182 ASP cc_start: 0.9143 (t0) cc_final: 0.8688 (t0) outliers start: 38 outliers final: 16 residues processed: 237 average time/residue: 0.6057 time to fit residues: 153.1350 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 9.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 304 ASN ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3667 r_free = 0.3667 target = 0.122159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.082565 restraints weight = 17098.991| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.63 r_work: 0.2851 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10242 Z= 0.147 Angle : 0.613 7.396 13941 Z= 0.309 Chirality : 0.041 0.156 1758 Planarity : 0.004 0.027 1617 Dihedral : 5.689 53.059 2469 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.62 % Allowed : 14.19 % Favored : 82.19 % 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: 1.14 (0.25), residues: 1098 helix: 1.26 (0.22), residues: 528 sheet: 0.60 (0.45), residues: 105 loop : 0.37 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 183 TYR 0.011 0.001 TYR C 156 PHE 0.021 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 covalent geometry : bond 0.00312 (10164) covalent geometry : angle 0.57697 (13722) SS BOND : bond 0.00666 ( 15) SS BOND : angle 1.28559 ( 30) hydrogen bonds : bond 0.04895 ( 486) hydrogen bonds : angle 4.95145 ( 1377) link_ALPHA1-2 : bond 0.00660 ( 3) link_ALPHA1-2 : angle 1.23668 ( 9) link_ALPHA1-3 : bond 0.00777 ( 6) link_ALPHA1-3 : angle 1.56206 ( 18) link_ALPHA1-6 : bond 0.00594 ( 6) link_ALPHA1-6 : angle 1.62486 ( 18) link_BETA1-4 : bond 0.00368 ( 15) link_BETA1-4 : angle 1.52223 ( 45) link_BETA1-6 : bond 0.00061 ( 3) link_BETA1-6 : angle 1.44817 ( 9) link_NAG-ASN : bond 0.00286 ( 30) link_NAG-ASN : angle 2.09886 ( 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 231 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.400 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: 0.7859 (t0) cc_final: 0.7486 (t0) REVERT: A 155 GLU cc_start: 0.8430 (tt0) cc_final: 0.8220 (tt0) REVERT: A 168 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: A 218 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8170 (mtp85) REVERT: A 219 LYS cc_start: 0.8595 (tptp) cc_final: 0.8299 (tptp) REVERT: B 120 ASP cc_start: 0.7956 (t0) cc_final: 0.7586 (t0) REVERT: B 144 LYS cc_start: 0.8258 (mtpt) cc_final: 0.8048 (mtpp) REVERT: B 196 THR cc_start: 0.8738 (m) cc_final: 0.8393 (p) REVERT: B 218 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8488 (mtm180) REVERT: B 219 LYS cc_start: 0.8556 (tptp) cc_final: 0.8249 (tptp) REVERT: C 120 ASP cc_start: 0.7925 (t0) cc_final: 0.7542 (t0) REVERT: C 155 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 168 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: C 182 ASP cc_start: 0.9104 (t0) cc_final: 0.8664 (t0) REVERT: SB 25 MET cc_start: 0.8334 (mmm) cc_final: 0.8061 (mmm) outliers start: 38 outliers final: 20 residues processed: 211 average time/residue: 0.5626 time to fit residues: 127.1644 Evaluate side-chains 209 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 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 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 SC residue 35 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 294 SER 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: 1.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN c 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080480 restraints weight = 17319.448| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.56 r_work: 0.2818 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10242 Z= 0.211 Angle : 0.648 8.704 13941 Z= 0.323 Chirality : 0.042 0.139 1758 Planarity : 0.004 0.044 1617 Dihedral : 5.812 54.936 2469 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.43 % Allowed : 16.29 % Favored : 80.29 % 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: 1.17 (0.26), residues: 1098 helix: 1.44 (0.23), residues: 528 sheet: 0.11 (0.45), residues: 123 loop : 0.33 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 218 TYR 0.012 0.002 TYR C 156 PHE 0.018 0.001 PHE a 402 TRP 0.017 0.002 TRP b 348 HIS 0.005 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00489 (10164) covalent geometry : angle 0.61007 (13722) SS BOND : bond 0.00460 ( 15) SS BOND : angle 1.55079 ( 30) hydrogen bonds : bond 0.04999 ( 486) hydrogen bonds : angle 4.87718 ( 1377) link_ALPHA1-2 : bond 0.00552 ( 3) link_ALPHA1-2 : angle 1.30775 ( 9) link_ALPHA1-3 : bond 0.00706 ( 6) link_ALPHA1-3 : angle 1.67630 ( 18) link_ALPHA1-6 : bond 0.00549 ( 6) link_ALPHA1-6 : angle 1.60133 ( 18) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 1.59878 ( 45) link_BETA1-6 : bond 0.00120 ( 3) link_BETA1-6 : angle 1.51942 ( 9) link_NAG-ASN : bond 0.00376 ( 30) link_NAG-ASN : angle 2.19767 ( 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 228 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8301 (t0) cc_final: 0.7911 (t0) REVERT: B 120 ASP cc_start: 0.8224 (t0) cc_final: 0.7822 (t0) REVERT: B 121 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7652 (mtp-110) REVERT: B 144 LYS cc_start: 0.8490 (mtpt) cc_final: 0.7903 (mtpp) REVERT: B 182 ASP cc_start: 0.8785 (t0) cc_final: 0.8484 (t0) REVERT: B 196 THR cc_start: 0.9009 (m) cc_final: 0.8696 (p) REVERT: C 120 ASP cc_start: 0.8271 (t0) cc_final: 0.7824 (t0) REVERT: C 155 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7758 (mt-10) REVERT: C 168 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: C 182 ASP cc_start: 0.9127 (t0) cc_final: 0.8668 (t0) REVERT: SB 25 MET cc_start: 0.8380 (mmm) cc_final: 0.8099 (mmm) outliers start: 36 outliers final: 18 residues processed: 209 average time/residue: 0.5274 time to fit residues: 118.0392 Evaluate side-chains 196 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3629 r_free = 0.3629 target = 0.120374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080579 restraints weight = 17227.991| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.61 r_work: 0.2798 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10242 Z= 0.165 Angle : 0.616 9.789 13941 Z= 0.308 Chirality : 0.040 0.149 1758 Planarity : 0.004 0.033 1617 Dihedral : 5.711 53.940 2469 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.52 % Allowed : 17.81 % 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: 1.26 (0.26), residues: 1098 helix: 1.59 (0.23), residues: 528 sheet: 0.22 (0.45), residues: 123 loop : 0.24 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 121 TYR 0.012 0.001 TYR C 156 PHE 0.015 0.001 PHE b 402 TRP 0.010 0.001 TRP b 348 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00370 (10164) covalent geometry : angle 0.58212 (13722) SS BOND : bond 0.00402 ( 15) SS BOND : angle 1.25491 ( 30) hydrogen bonds : bond 0.04737 ( 486) hydrogen bonds : angle 4.74342 ( 1377) link_ALPHA1-2 : bond 0.00606 ( 3) link_ALPHA1-2 : angle 1.27127 ( 9) link_ALPHA1-3 : bond 0.00748 ( 6) link_ALPHA1-3 : angle 1.55050 ( 18) link_ALPHA1-6 : bond 0.00590 ( 6) link_ALPHA1-6 : angle 1.60089 ( 18) link_BETA1-4 : bond 0.00383 ( 15) link_BETA1-4 : angle 1.47949 ( 45) link_BETA1-6 : bond 0.00029 ( 3) link_BETA1-6 : angle 1.46052 ( 9) link_NAG-ASN : bond 0.00220 ( 30) link_NAG-ASN : angle 2.03340 ( 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 225 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8297 (t0) cc_final: 0.7912 (t0) REVERT: A 155 GLU cc_start: 0.8617 (tt0) cc_final: 0.8362 (tt0) REVERT: A 168 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 218 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8722 (mtp85) REVERT: A 219 LYS cc_start: 0.8617 (tptp) cc_final: 0.8357 (tptp) REVERT: a 281 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8875 (t0) REVERT: B 120 ASP cc_start: 0.8265 (t0) cc_final: 0.7835 (t0) REVERT: B 121 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7547 (mtp-110) REVERT: B 182 ASP cc_start: 0.8886 (t0) cc_final: 0.8518 (t0) REVERT: B 196 THR cc_start: 0.9004 (m) cc_final: 0.8702 (p) REVERT: B 218 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8473 (mtm180) REVERT: B 219 LYS cc_start: 0.8623 (tptp) cc_final: 0.8390 (tptp) REVERT: C 105 LYS cc_start: 0.9383 (tttm) cc_final: 0.9168 (tttp) REVERT: C 120 ASP cc_start: 0.8349 (t0) cc_final: 0.7843 (t0) REVERT: C 155 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7822 (mt-10) REVERT: C 168 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: C 182 ASP cc_start: 0.9118 (t0) cc_final: 0.8660 (t0) REVERT: C 219 LYS cc_start: 0.8642 (tptp) cc_final: 0.8363 (tptp) REVERT: SB 25 MET cc_start: 0.8406 (mmm) cc_final: 0.8135 (mmm) outliers start: 37 outliers final: 20 residues processed: 211 average time/residue: 0.5621 time to fit residues: 126.4447 Evaluate side-chains 209 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.081436 restraints weight = 17321.258| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.61 r_work: 0.2817 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10242 Z= 0.134 Angle : 0.607 10.602 13941 Z= 0.300 Chirality : 0.039 0.151 1758 Planarity : 0.004 0.035 1617 Dihedral : 5.628 53.419 2469 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.00 % Allowed : 17.81 % Favored : 78.19 % 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: 1.32 (0.26), residues: 1098 helix: 1.67 (0.23), residues: 528 sheet: 0.32 (0.45), residues: 123 loop : 0.18 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 244 TYR 0.013 0.001 TYR C 156 PHE 0.013 0.001 PHE b 402 TRP 0.007 0.001 TRP b 226 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00300 (10164) covalent geometry : angle 0.57527 (13722) SS BOND : bond 0.00331 ( 15) SS BOND : angle 1.17716 ( 30) hydrogen bonds : bond 0.04461 ( 486) hydrogen bonds : angle 4.66712 ( 1377) link_ALPHA1-2 : bond 0.00593 ( 3) link_ALPHA1-2 : angle 1.26845 ( 9) link_ALPHA1-3 : bond 0.00847 ( 6) link_ALPHA1-3 : angle 1.54961 ( 18) link_ALPHA1-6 : bond 0.00597 ( 6) link_ALPHA1-6 : angle 1.58809 ( 18) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.45361 ( 45) link_BETA1-6 : bond 0.00096 ( 3) link_BETA1-6 : angle 1.39073 ( 9) link_NAG-ASN : bond 0.00146 ( 30) link_NAG-ASN : angle 1.93623 ( 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 234 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8313 (t0) cc_final: 0.7905 (t0) REVERT: A 155 GLU cc_start: 0.8570 (tt0) cc_final: 0.8358 (tt0) REVERT: A 168 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: A 218 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8609 (mtp85) REVERT: A 219 LYS cc_start: 0.8658 (tptp) cc_final: 0.8360 (tptp) REVERT: a 281 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8826 (t0) REVERT: B 120 ASP cc_start: 0.8217 (t0) cc_final: 0.7797 (t0) REVERT: B 121 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7563 (mtp-110) REVERT: B 144 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8245 (mtpp) REVERT: B 182 ASP cc_start: 0.8914 (t0) cc_final: 0.8528 (t0) REVERT: B 196 THR cc_start: 0.9007 (m) cc_final: 0.8733 (p) REVERT: B 218 ARG cc_start: 0.8724 (mtm180) cc_final: 0.8297 (mmm160) REVERT: B 219 LYS cc_start: 0.8630 (tptp) cc_final: 0.8390 (tptp) REVERT: C 105 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9108 (tmtm) REVERT: C 120 ASP cc_start: 0.8335 (t0) cc_final: 0.7834 (t0) REVERT: C 155 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 168 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: C 182 ASP cc_start: 0.9074 (t0) cc_final: 0.8632 (t0) REVERT: C 219 LYS cc_start: 0.8643 (tptp) cc_final: 0.8335 (tptp) REVERT: SB 25 MET cc_start: 0.8366 (mmm) cc_final: 0.8091 (mmm) outliers start: 42 outliers final: 20 residues processed: 218 average time/residue: 0.5296 time to fit residues: 123.3151 Evaluate side-chains 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 C residue 105 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE 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 SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 255 PHE 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: 2.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 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 = 0.3625 r_free = 0.3625 target = 0.119875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080566 restraints weight = 17253.401| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.58 r_work: 0.2798 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10242 Z= 0.165 Angle : 0.635 11.205 13941 Z= 0.313 Chirality : 0.040 0.182 1758 Planarity : 0.004 0.036 1617 Dihedral : 5.653 54.104 2469 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.62 % Allowed : 18.95 % Favored : 77.43 % 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: 1.33 (0.26), residues: 1098 helix: 1.68 (0.23), residues: 528 sheet: 0.39 (0.46), residues: 123 loop : 0.16 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 244 TYR 0.013 0.001 TYR C 156 PHE 0.015 0.001 PHE a 361 TRP 0.008 0.001 TRP b 348 HIS 0.002 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00377 (10164) covalent geometry : angle 0.60392 (13722) SS BOND : bond 0.00371 ( 15) SS BOND : angle 1.29050 ( 30) hydrogen bonds : bond 0.04578 ( 486) hydrogen bonds : angle 4.69594 ( 1377) link_ALPHA1-2 : bond 0.00557 ( 3) link_ALPHA1-2 : angle 1.30485 ( 9) link_ALPHA1-3 : bond 0.00739 ( 6) link_ALPHA1-3 : angle 1.54868 ( 18) link_ALPHA1-6 : bond 0.00567 ( 6) link_ALPHA1-6 : angle 1.56835 ( 18) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.48963 ( 45) link_BETA1-6 : bond 0.00036 ( 3) link_BETA1-6 : angle 1.43295 ( 9) link_NAG-ASN : bond 0.00205 ( 30) link_NAG-ASN : angle 1.98210 ( 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 227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8384 (t0) cc_final: 0.7948 (t0) REVERT: A 159 THR cc_start: 0.8652 (t) cc_final: 0.8450 (p) REVERT: A 168 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: A 218 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8669 (mtp85) REVERT: A 219 LYS cc_start: 0.8715 (tptp) cc_final: 0.8449 (tptp) REVERT: a 281 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8842 (t0) REVERT: a 313 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8452 (mtm) REVERT: B 120 ASP cc_start: 0.8370 (t0) cc_final: 0.7924 (t0) REVERT: B 121 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7637 (mtp-110) REVERT: B 196 THR cc_start: 0.9044 (m) cc_final: 0.8780 (p) REVERT: B 218 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8437 (mtm180) REVERT: B 219 LYS cc_start: 0.8678 (tptp) cc_final: 0.8468 (tptp) REVERT: C 120 ASP cc_start: 0.8394 (t0) cc_final: 0.7891 (t0) REVERT: C 144 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7749 (mtpp) REVERT: C 155 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 159 THR cc_start: 0.8559 (t) cc_final: 0.8349 (p) REVERT: C 168 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: C 182 ASP cc_start: 0.9045 (t0) cc_final: 0.8606 (t0) REVERT: C 219 LYS cc_start: 0.8684 (tptp) cc_final: 0.8419 (tptp) REVERT: SB 25 MET cc_start: 0.8401 (mmm) cc_final: 0.8126 (mmm) outliers start: 38 outliers final: 21 residues processed: 209 average time/residue: 0.5471 time to fit residues: 122.2648 Evaluate side-chains 211 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 a residue 296 ILE Chi-restraints excluded: chain a residue 313 MET 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 C residue 114 THR Chi-restraints excluded: chain C residue 144 LYS 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 SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 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 = 0.3614 r_free = 0.3614 target = 0.119299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080097 restraints weight = 17196.816| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.54 r_work: 0.2785 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10242 Z= 0.179 Angle : 0.646 12.273 13941 Z= 0.318 Chirality : 0.041 0.198 1758 Planarity : 0.004 0.037 1617 Dihedral : 5.679 54.224 2469 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.62 % Allowed : 20.19 % Favored : 76.19 % 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: 1.36 (0.26), residues: 1098 helix: 1.72 (0.23), residues: 528 sheet: 0.46 (0.46), residues: 123 loop : 0.13 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 244 TYR 0.012 0.001 TYR C 156 PHE 0.012 0.001 PHE C 127 TRP 0.008 0.001 TRP b 348 HIS 0.002 0.000 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00411 (10164) covalent geometry : angle 0.61497 (13722) SS BOND : bond 0.00389 ( 15) SS BOND : angle 1.28226 ( 30) hydrogen bonds : bond 0.04628 ( 486) hydrogen bonds : angle 4.72950 ( 1377) link_ALPHA1-2 : bond 0.00536 ( 3) link_ALPHA1-2 : angle 1.30872 ( 9) link_ALPHA1-3 : bond 0.00734 ( 6) link_ALPHA1-3 : angle 1.55204 ( 18) link_ALPHA1-6 : bond 0.00563 ( 6) link_ALPHA1-6 : angle 1.55251 ( 18) link_BETA1-4 : bond 0.00356 ( 15) link_BETA1-4 : angle 1.47756 ( 45) link_BETA1-6 : bond 0.00037 ( 3) link_BETA1-6 : angle 1.46169 ( 9) link_NAG-ASN : bond 0.00232 ( 30) link_NAG-ASN : angle 2.00808 ( 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 223 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8398 (t0) cc_final: 0.7953 (t0) REVERT: A 121 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7723 (tpp80) REVERT: A 144 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7679 (mtpm) REVERT: A 168 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: A 218 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8634 (mtp85) REVERT: A 219 LYS cc_start: 0.8707 (tptp) cc_final: 0.8436 (tptp) REVERT: a 281 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8836 (t0) REVERT: a 313 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: B 120 ASP cc_start: 0.8386 (t0) cc_final: 0.7902 (t0) REVERT: B 121 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7663 (mtp-110) REVERT: B 144 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7604 (mtpp) REVERT: B 196 THR cc_start: 0.9047 (m) cc_final: 0.8800 (p) REVERT: B 218 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8393 (mtm180) REVERT: B 219 LYS cc_start: 0.8671 (tptp) cc_final: 0.8463 (tptp) REVERT: C 105 LYS cc_start: 0.9395 (tttp) cc_final: 0.9117 (tmtm) REVERT: C 120 ASP cc_start: 0.8425 (t0) cc_final: 0.7909 (t0) REVERT: C 144 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7603 (mtpp) REVERT: C 155 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7801 (mt-10) REVERT: C 159 THR cc_start: 0.8562 (t) cc_final: 0.8357 (p) REVERT: C 182 ASP cc_start: 0.9074 (t0) cc_final: 0.8638 (t0) REVERT: SB 25 MET cc_start: 0.8492 (mmm) cc_final: 0.8226 (mmm) outliers start: 38 outliers final: 22 residues processed: 208 average time/residue: 0.5603 time to fit residues: 123.9884 Evaluate side-chains 207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 a residue 313 MET 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 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 144 LYS Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL 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 c residue 255 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 34 ASN B 86 GLN C 86 GLN C 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080978 restraints weight = 17412.562| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.58 r_work: 0.2827 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10242 Z= 0.137 Angle : 0.656 14.278 13941 Z= 0.321 Chirality : 0.040 0.210 1758 Planarity : 0.004 0.039 1617 Dihedral : 5.596 53.193 2469 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.57 % Allowed : 21.33 % Favored : 76.10 % 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: 1.38 (0.26), residues: 1098 helix: 1.75 (0.23), residues: 528 sheet: 0.58 (0.47), residues: 123 loop : 0.10 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 244 TYR 0.015 0.001 TYR b 403 PHE 0.013 0.001 PHE a 361 TRP 0.007 0.001 TRP c 226 HIS 0.003 0.000 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00307 (10164) covalent geometry : angle 0.62869 (13722) SS BOND : bond 0.00322 ( 15) SS BOND : angle 1.16856 ( 30) hydrogen bonds : bond 0.04410 ( 486) hydrogen bonds : angle 4.63476 ( 1377) link_ALPHA1-2 : bond 0.00559 ( 3) link_ALPHA1-2 : angle 1.28366 ( 9) link_ALPHA1-3 : bond 0.00845 ( 6) link_ALPHA1-3 : angle 1.52897 ( 18) link_ALPHA1-6 : bond 0.00591 ( 6) link_ALPHA1-6 : angle 1.54596 ( 18) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.43308 ( 45) link_BETA1-6 : bond 0.00089 ( 3) link_BETA1-6 : angle 1.37779 ( 9) link_NAG-ASN : bond 0.00139 ( 30) link_NAG-ASN : angle 1.89331 ( 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 213 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8475 (t0) cc_final: 0.8090 (t0) REVERT: A 121 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7761 (tpp80) REVERT: A 144 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7696 (mtpm) REVERT: A 168 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 218 ARG cc_start: 0.9032 (mtp85) cc_final: 0.8558 (mtp85) REVERT: A 219 LYS cc_start: 0.8720 (tptp) cc_final: 0.8404 (tptp) REVERT: a 281 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8919 (t0) REVERT: B 120 ASP cc_start: 0.8419 (t0) cc_final: 0.8007 (t0) REVERT: B 121 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7953 (tpp80) REVERT: B 144 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8185 (mtpp) REVERT: B 196 THR cc_start: 0.9141 (m) cc_final: 0.8930 (p) REVERT: B 218 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8353 (mtm180) REVERT: B 219 LYS cc_start: 0.8721 (tptp) cc_final: 0.8476 (tptp) REVERT: C 105 LYS cc_start: 0.9353 (tttp) cc_final: 0.9083 (tmtm) REVERT: C 120 ASP cc_start: 0.8517 (t0) cc_final: 0.8064 (t0) REVERT: C 144 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7876 (mtpp) REVERT: C 155 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 182 ASP cc_start: 0.9048 (t0) cc_final: 0.8615 (t0) REVERT: SB 25 MET cc_start: 0.8450 (mmm) cc_final: 0.8197 (mmm) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.5595 time to fit residues: 122.2442 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 281 ASN Chi-restraints excluded: chain a residue 294 SER 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 C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 174 PHE 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 c residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079666 restraints weight = 17414.845| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.59 r_work: 0.2797 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10242 Z= 0.168 Angle : 0.668 13.838 13941 Z= 0.328 Chirality : 0.040 0.203 1758 Planarity : 0.004 0.040 1617 Dihedral : 5.634 54.251 2469 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.67 % Allowed : 22.00 % Favored : 75.33 % 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: 1.38 (0.26), residues: 1098 helix: 1.75 (0.23), residues: 528 sheet: 0.63 (0.48), residues: 123 loop : 0.07 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 244 TYR 0.012 0.001 TYR C 156 PHE 0.009 0.001 PHE C 127 TRP 0.007 0.001 TRP c 226 HIS 0.003 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00384 (10164) covalent geometry : angle 0.63916 (13722) SS BOND : bond 0.00360 ( 15) SS BOND : angle 1.27707 ( 30) hydrogen bonds : bond 0.04576 ( 486) hydrogen bonds : angle 4.70092 ( 1377) link_ALPHA1-2 : bond 0.00518 ( 3) link_ALPHA1-2 : angle 1.32719 ( 9) link_ALPHA1-3 : bond 0.00703 ( 6) link_ALPHA1-3 : angle 1.53650 ( 18) link_ALPHA1-6 : bond 0.00555 ( 6) link_ALPHA1-6 : angle 1.52759 ( 18) link_BETA1-4 : bond 0.00344 ( 15) link_BETA1-4 : angle 1.47571 ( 45) link_BETA1-6 : bond 0.00016 ( 3) link_BETA1-6 : angle 1.43567 ( 9) link_NAG-ASN : bond 0.00206 ( 30) link_NAG-ASN : angle 1.95224 ( 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 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8536 (t0) cc_final: 0.8228 (t0) REVERT: A 121 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7725 (tpp80) REVERT: A 144 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7751 (mtpm) REVERT: A 168 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 218 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8724 (mtp85) REVERT: A 219 LYS cc_start: 0.8745 (tptp) cc_final: 0.8475 (tptp) REVERT: a 281 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8995 (t0) REVERT: B 120 ASP cc_start: 0.8482 (t0) cc_final: 0.8044 (t0) REVERT: B 121 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7847 (mtp-110) REVERT: B 144 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7581 (mtpp) REVERT: B 218 ARG cc_start: 0.8758 (mtm180) cc_final: 0.8429 (mtm180) REVERT: B 219 LYS cc_start: 0.8752 (tptp) cc_final: 0.8547 (tptp) REVERT: C 105 LYS cc_start: 0.9364 (tttp) cc_final: 0.9088 (tmtm) REVERT: C 120 ASP cc_start: 0.8607 (t0) cc_final: 0.8136 (t0) REVERT: C 144 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7827 (mtpp) REVERT: C 182 ASP cc_start: 0.9081 (t0) cc_final: 0.8691 (t0) REVERT: SB 25 MET cc_start: 0.8539 (mmm) cc_final: 0.8286 (mmm) REVERT: c 268 ASP cc_start: 0.8643 (t70) cc_final: 0.8298 (t0) REVERT: c 364 ASP cc_start: 0.8947 (m-30) cc_final: 0.8547 (t0) outliers start: 28 outliers final: 20 residues processed: 204 average time/residue: 0.5534 time to fit residues: 120.0377 Evaluate side-chains 194 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 139 VAL 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 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 182 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 255 PHE Chi-restraints excluded: chain b residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080609 restraints weight = 17600.164| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.57 r_work: 0.2818 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4293 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= 0.138 Angle : 0.655 13.682 13941 Z= 0.322 Chirality : 0.040 0.211 1758 Planarity : 0.004 0.041 1617 Dihedral : 5.576 53.585 2469 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.67 % Allowed : 22.29 % Favored : 75.05 % 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: 1.78 (0.23), residues: 528 sheet: 0.68 (0.48), residues: 123 loop : 0.08 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 244 TYR 0.011 0.001 TYR C 156 PHE 0.010 0.001 PHE a 361 TRP 0.008 0.001 TRP c 226 HIS 0.004 0.000 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00308 (10164) covalent geometry : angle 0.62769 (13722) SS BOND : bond 0.00321 ( 15) SS BOND : angle 1.18569 ( 30) hydrogen bonds : bond 0.04433 ( 486) hydrogen bonds : angle 4.66361 ( 1377) link_ALPHA1-2 : bond 0.00572 ( 3) link_ALPHA1-2 : angle 1.31499 ( 9) link_ALPHA1-3 : bond 0.00757 ( 6) link_ALPHA1-3 : angle 1.49968 ( 18) link_ALPHA1-6 : bond 0.00581 ( 6) link_ALPHA1-6 : angle 1.52721 ( 18) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.43865 ( 45) link_BETA1-6 : bond 0.00084 ( 3) link_BETA1-6 : angle 1.39545 ( 9) link_NAG-ASN : bond 0.00138 ( 30) link_NAG-ASN : angle 1.89193 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.58 seconds wall clock time: 58 minutes 28.71 seconds (3508.71 seconds total)