Starting phenix.real_space_refine on Thu Nov 20 02:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.cif Found real_map, /net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6be1_7088/11_2025/6be1_7088.map" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15500 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 S 50 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 11052 2.51 5 N 2701 2.21 5 O 3100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16910 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3277 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3265 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3272 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3266 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3269 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'PX4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PX4:plan-2': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CL': 1, 'NAG': 2, 'PX4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'BMA': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.16, per 1000 atoms: 0.25 Number of scatterers: 16910 At special positions: 0 Unit cell: (106.4, 103.208, 177.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 50 16.00 P 5 15.00 Na 1 11.00 O 3100 8.00 N 2701 7.00 C 11052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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=4, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " " NAG M 2 " - " BMA M 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG C 506 " - " ASN C 148 " " NAG D 504 " - " ASN D 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN B 148 " " NAG K 1 " - " ASN C 164 " " NAG L 1 " - " ASN C 82 " " NAG M 1 " - " ASN D 164 " " NAG N 1 " - " ASN D 148 " " NAG O 1 " - " ASN E 164 " " NAG P 1 " - " ASN E 82 " " NAG Q 1 " - " ASN E 148 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 598.4 milliseconds 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 38.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.588A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 5.788A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.512A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 308 removed outlier: 4.238A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 399 through 457 removed outlier: 3.938A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.965A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.580A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 5.744A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 250 through 269 Processing helix chain 'B' and resid 282 through 308 removed outlier: 4.182A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.752A pdb=" N ARG B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 462 removed outlier: 4.597A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 4.225A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.646A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'C' and resid 250 through 269 Processing helix chain 'C' and resid 282 through 308 removed outlier: 3.683A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 325 removed outlier: 3.744A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 405 Processing helix chain 'C' and resid 406 through 461 removed outlier: 3.883A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 removed outlier: 3.982A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.981A pdb=" N SER D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 223 through 242 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 250 through 271 removed outlier: 4.455A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 284 through 308 Processing helix chain 'D' and resid 318 through 326 removed outlier: 3.624A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 402 through 458 removed outlier: 3.893A pdb=" N LEU D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 4.343A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.501A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 228 removed outlier: 3.577A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 Processing helix chain 'E' and resid 249 through 269 removed outlier: 3.815A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 removed outlier: 3.998A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.647A pdb=" N TRP E 320 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 457 removed outlier: 3.731A pdb=" N SER E 407 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.523A pdb=" N LYS A 127 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 64 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 129 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 62 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.523A pdb=" N LYS A 127 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 64 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 129 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 62 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 59 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TRP A 63 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N MET A 45 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG A 65 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR A 67 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 41 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.746A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 147 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.746A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 190 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.231A pdb=" N PHE A 199 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 201 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.823A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 125 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP B 68 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 123 " --> pdb=" O TRP B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.823A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 57 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 51 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 59 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 63 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N MET B 45 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG B 65 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 67 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE B 41 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL B 39 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 196 removed outlier: 7.147A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.176A pdb=" N PHE B 199 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 201 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 122 through 125 removed outlier: 3.673A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE C 62 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 129 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 125 removed outlier: 3.673A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.531A pdb=" N THR C 154 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 149 through 150 removed outlier: 4.121A pdb=" N CYS C 149 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 214 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 193 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.507A pdb=" N PHE C 199 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 207 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 201 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.888A pdb=" N GLN D 124 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 62 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 129 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.888A pdb=" N GLN D 124 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D 59 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 47 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP D 63 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET D 45 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG D 65 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 67 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 41 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.774A pdb=" N GLN D 147 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 151 through 154 removed outlier: 7.661A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 86 through 89 removed outlier: 6.930A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN E 124 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 125 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 129 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE E 62 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL E 57 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL E 51 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR E 59 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TRP E 63 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N MET E 45 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG E 65 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR E 67 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE E 41 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 164 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 187 through 196 removed outlier: 5.648A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE E 215 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 199 through 202 removed outlier: 4.727A pdb=" N PHE E 199 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR E 207 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE E 201 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 660 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2593 1.32 - 1.44: 4952 1.44 - 1.56: 9698 1.56 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 17338 Sorted by residual: bond pdb=" O2 PX4 E 508 " pdb=" P1 PX4 E 508 " ideal model delta sigma weight residual 1.497 1.691 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" O2 PX4 A 509 " pdb=" P1 PX4 A 509 " ideal model delta sigma weight residual 1.497 1.691 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" O3 PX4 E 508 " pdb=" P1 PX4 E 508 " ideal model delta sigma weight residual 1.649 1.465 0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" O3 PX4 A 509 " pdb=" P1 PX4 A 509 " ideal model delta sigma weight residual 1.649 1.465 0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" C9 PX4 A 509 " pdb=" O5 PX4 A 509 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 17333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.80: 23502 5.80 - 11.60: 146 11.60 - 17.41: 17 17.41 - 23.21: 6 23.21 - 29.01: 4 Bond angle restraints: 23675 Sorted by residual: angle pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " pdb=" O4 NAG G 1 " ideal model delta sigma weight residual 107.29 136.30 -29.01 3.00e+00 1.11e-01 9.35e+01 angle pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 107.29 136.10 -28.81 3.00e+00 1.11e-01 9.22e+01 angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 135.66 -28.37 3.00e+00 1.11e-01 8.94e+01 angle pdb=" C5 NAG P 1 " pdb=" C4 NAG P 1 " pdb=" O4 NAG P 1 " ideal model delta sigma weight residual 111.70 138.91 -27.21 3.00e+00 1.11e-01 8.23e+01 angle pdb=" C4 NAG M 2 " pdb=" C3 NAG M 2 " pdb=" O3 NAG M 2 " ideal model delta sigma weight residual 112.02 89.19 22.83 3.00e+00 1.11e-01 5.79e+01 ... (remaining 23670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 10310 32.68 - 65.36: 272 65.36 - 98.04: 61 98.04 - 130.72: 27 130.72 - 163.40: 4 Dihedral angle restraints: 10674 sinusoidal: 4729 harmonic: 5945 Sorted by residual: dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 147.42 -54.42 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 144.31 -51.31 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 143.56 -50.56 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 10671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.808: 2814 0.808 - 1.616: 0 1.616 - 2.424: 1 2.424 - 3.232: 3 3.232 - 4.039: 1 Chirality restraints: 2819 Sorted by residual: chirality pdb=" C4 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O4 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.53 1.51 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 0.69 -3.22 2.00e-01 2.50e+01 2.60e+02 chirality pdb=" C4 NAG P 1 " pdb=" C3 NAG P 1 " pdb=" C5 NAG P 1 " pdb=" O4 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.53 0.69 -3.22 2.00e-01 2.50e+01 2.59e+02 ... (remaining 2816 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 213 " 0.016 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR E 213 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 213 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 213 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 213 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 213 " 0.045 2.00e-02 2.50e+03 pdb=" CZ TYR E 213 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 213 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 280 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO D 281 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 233 " 0.021 2.00e-02 2.50e+03 1.77e-02 5.51e+00 pdb=" CG PHE A 233 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 233 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 233 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 233 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 233 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 233 " -0.000 2.00e-02 2.50e+03 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4669 2.82 - 3.34: 14246 3.34 - 3.86: 27519 3.86 - 4.38: 27831 4.38 - 4.90: 48643 Nonbonded interactions: 122908 Sorted by model distance: nonbonded pdb=" O ALA D 47 " pdb=" OG1 THR D 60 " model vdw 2.301 3.040 nonbonded pdb=" O VAL C 39 " pdb=" OG1 THR C 166 " model vdw 2.334 3.040 nonbonded pdb=" OH TYR D 116 " pdb=" O LEU E 157 " model vdw 2.336 3.040 nonbonded pdb=" O ALA E 47 " pdb=" OG1 THR E 60 " model vdw 2.341 3.040 nonbonded pdb=" O PHE C 222 " pdb=" OG SER C 226 " model vdw 2.342 3.040 ... (remaining 122903 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 6 through 318 or (resid 319 and (name N or name CA or name \ C or name O or name CB )) or resid 320 through 322 or (resid 323 through 326 an \ d (name N or name CA or name C or name O or name CB )) or resid 327 through 332 \ or (resid 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 338 or (resid 397 through 399 and (name N or name CA or name C or na \ me O or name CB )) or resid 400 through 462)) selection = (chain 'B' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 398 or (resid 399 and (name N or \ name CA or name C or name O or name CB )) or resid 400 through 462)) selection = (chain 'C' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 318 or (resid 319 and (name N or \ name CA or name C or name O or name CB )) or resid 320 through 325 or (resid 32 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 327 through \ 338 or (resid 397 through 399 and (name N or name CA or name C or name O or name \ CB )) or resid 400 through 462)) selection = (chain 'D' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 338 or (resid 397 through 399 an \ d (name N or name CA or name C or name O or name CB )) or resid 400 through 462) \ ) selection = (chain 'E' and (resid 6 through 311 or (resid 312 and (name N or name CA or name \ C or name O or name CB )) or resid 313 through 318 or (resid 319 and (name N or \ name CA or name C or name O or name CB )) or resid 320 through 338 or (resid 39 \ 7 through 399 and (name N or name CA or name C or name O or name CB )) or resid \ 400 through 462)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.950 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.007 0.194 17377 Z= 0.337 Angle : 1.414 51.056 23775 Z= 0.631 Chirality : 0.146 4.039 2819 Planarity : 0.007 0.067 2872 Dihedral : 16.375 163.399 6789 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.66 % Allowed : 8.45 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.15), residues: 1975 helix: -2.07 (0.15), residues: 705 sheet: -2.56 (0.26), residues: 320 loop : -3.72 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 28 TYR 0.045 0.002 TYR E 213 PHE 0.039 0.003 PHE A 233 TRP 0.021 0.001 TRP A 68 HIS 0.005 0.001 HIS E 158 Details of bonding type rmsd covalent geometry : bond 0.00644 (17338) covalent geometry : angle 1.27799 (23675) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.59815 ( 10) hydrogen bonds : bond 0.15541 ( 648) hydrogen bonds : angle 6.72392 ( 1947) Misc. bond : bond 0.00928 ( 4) link_BETA1-3 : bond 0.02440 ( 2) link_BETA1-3 : angle 11.43603 ( 6) link_BETA1-4 : bond 0.03232 ( 14) link_BETA1-4 : angle 13.57636 ( 42) link_NAG-ASN : bond 0.00385 ( 14) link_NAG-ASN : angle 2.69478 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 353 time to evaluate : 0.549 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.8908 (m) cc_final: 0.8667 (p) REVERT: A 221 LEU cc_start: 0.7971 (mm) cc_final: 0.7759 (pp) REVERT: A 247 ASP cc_start: 0.8169 (m-30) cc_final: 0.7766 (t0) REVERT: A 254 PHE cc_start: 0.8674 (t80) cc_final: 0.8405 (t80) REVERT: A 434 ASP cc_start: 0.8539 (t0) cc_final: 0.8233 (t70) REVERT: A 436 LEU cc_start: 0.9137 (pp) cc_final: 0.8608 (mt) REVERT: B 42 ASP cc_start: 0.7693 (t70) cc_final: 0.7463 (t0) REVERT: B 165 ILE cc_start: 0.9447 (mp) cc_final: 0.9113 (pt) REVERT: B 247 ASP cc_start: 0.8028 (m-30) cc_final: 0.7795 (t0) REVERT: B 254 PHE cc_start: 0.9135 (t80) cc_final: 0.8895 (t80) REVERT: B 305 VAL cc_start: 0.9340 (t) cc_final: 0.9090 (m) REVERT: C 105 ASP cc_start: 0.7992 (t0) cc_final: 0.7781 (t0) REVERT: C 221 LEU cc_start: 0.8176 (mm) cc_final: 0.7639 (tp) REVERT: C 254 PHE cc_start: 0.8737 (t80) cc_final: 0.8428 (t80) REVERT: C 305 VAL cc_start: 0.9426 (t) cc_final: 0.9222 (m) REVERT: C 436 LEU cc_start: 0.9108 (pp) cc_final: 0.8490 (mt) REVERT: D 254 PHE cc_start: 0.8867 (t80) cc_final: 0.8234 (t80) REVERT: D 257 THR cc_start: 0.9205 (m) cc_final: 0.8913 (p) REVERT: D 305 VAL cc_start: 0.9326 (t) cc_final: 0.9112 (m) REVERT: D 411 HIS cc_start: 0.8314 (m90) cc_final: 0.8045 (m-70) REVERT: D 437 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8600 (pt) REVERT: E 247 ASP cc_start: 0.8222 (m-30) cc_final: 0.7772 (t0) REVERT: E 259 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9076 (tp) REVERT: E 305 VAL cc_start: 0.9288 (t) cc_final: 0.9077 (m) REVERT: E 436 LEU cc_start: 0.9181 (pp) cc_final: 0.8789 (mt) outliers start: 30 outliers final: 2 residues processed: 369 average time/residue: 0.1309 time to fit residues: 73.0839 Evaluate side-chains 181 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 124 GLN E 9 GLN E 56 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.087745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068196 restraints weight = 63268.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070127 restraints weight = 37068.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071098 restraints weight = 26073.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071980 restraints weight = 21176.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072309 restraints weight = 18167.694| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17377 Z= 0.159 Angle : 0.786 11.490 23775 Z= 0.374 Chirality : 0.050 0.304 2819 Planarity : 0.005 0.049 2872 Dihedral : 14.869 172.797 2958 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.83 % Allowed : 6.02 % Favored : 93.15 % 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: -2.99 (0.17), residues: 1975 helix: -0.30 (0.19), residues: 725 sheet: -2.33 (0.30), residues: 275 loop : -3.31 (0.16), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 120 TYR 0.024 0.001 TYR C 262 PHE 0.022 0.002 PHE D 412 TRP 0.019 0.001 TRP C 68 HIS 0.009 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00356 (17338) covalent geometry : angle 0.76625 (23675) SS BOND : bond 0.00578 ( 5) SS BOND : angle 0.54241 ( 10) hydrogen bonds : bond 0.04312 ( 648) hydrogen bonds : angle 4.98916 ( 1947) Misc. bond : bond 0.00338 ( 4) link_BETA1-3 : bond 0.01130 ( 2) link_BETA1-3 : angle 3.89427 ( 6) link_BETA1-4 : bond 0.00711 ( 14) link_BETA1-4 : angle 3.46606 ( 42) link_NAG-ASN : bond 0.00253 ( 14) link_NAG-ASN : angle 2.16724 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 0.691 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 revert: symmetry clash REVERT: A 38 THR cc_start: 0.8957 (m) cc_final: 0.8711 (p) REVERT: A 100 ILE cc_start: 0.8874 (pt) cc_final: 0.8673 (pt) REVERT: A 247 ASP cc_start: 0.8435 (m-30) cc_final: 0.7915 (t0) REVERT: A 254 PHE cc_start: 0.8751 (t80) cc_final: 0.8443 (t80) REVERT: A 433 LEU cc_start: 0.9290 (mt) cc_final: 0.9004 (mt) REVERT: A 436 LEU cc_start: 0.9176 (pp) cc_final: 0.8543 (mt) REVERT: B 42 ASP cc_start: 0.8060 (t70) cc_final: 0.7839 (t0) REVERT: B 254 PHE cc_start: 0.9226 (t80) cc_final: 0.8934 (t80) REVERT: C 210 MET cc_start: 0.8319 (ppp) cc_final: 0.7974 (ppp) REVERT: C 221 LEU cc_start: 0.8210 (mm) cc_final: 0.7570 (tp) REVERT: C 254 PHE cc_start: 0.8841 (t80) cc_final: 0.8533 (t80) REVERT: C 305 VAL cc_start: 0.9460 (t) cc_final: 0.9235 (m) REVERT: C 436 LEU cc_start: 0.9119 (pp) cc_final: 0.8525 (mt) REVERT: D 210 MET cc_start: 0.8118 (ppp) cc_final: 0.7864 (ppp) REVERT: D 254 PHE cc_start: 0.9019 (t80) cc_final: 0.8324 (t80) REVERT: D 331 TRP cc_start: 0.5123 (m100) cc_final: 0.4541 (m100) REVERT: E 247 ASP cc_start: 0.8345 (m-30) cc_final: 0.7972 (t0) REVERT: E 259 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9027 (tp) REVERT: E 413 LEU cc_start: 0.9329 (mt) cc_final: 0.8983 (mt) outliers start: 15 outliers final: 0 residues processed: 261 average time/residue: 0.1219 time to fit residues: 50.0902 Evaluate side-chains 160 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 11 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 188 optimal weight: 30.0000 chunk 157 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 144 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.065942 restraints weight = 63683.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067779 restraints weight = 36857.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069008 restraints weight = 25653.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069684 restraints weight = 20086.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069929 restraints weight = 17612.459| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17377 Z= 0.140 Angle : 0.751 9.716 23775 Z= 0.353 Chirality : 0.048 0.312 2819 Planarity : 0.004 0.048 2872 Dihedral : 13.115 172.205 2958 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.72 % Allowed : 5.19 % Favored : 94.09 % 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: -2.46 (0.18), residues: 1975 helix: 0.26 (0.20), residues: 725 sheet: -2.16 (0.28), residues: 325 loop : -3.09 (0.17), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.025 0.001 TYR C 262 PHE 0.016 0.001 PHE E 412 TRP 0.015 0.001 TRP C 68 HIS 0.006 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00313 (17338) covalent geometry : angle 0.73274 (23675) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.62871 ( 10) hydrogen bonds : bond 0.04166 ( 648) hydrogen bonds : angle 4.61306 ( 1947) Misc. bond : bond 0.00465 ( 4) link_BETA1-3 : bond 0.00907 ( 2) link_BETA1-3 : angle 3.37274 ( 6) link_BETA1-4 : bond 0.00694 ( 14) link_BETA1-4 : angle 3.28553 ( 42) link_NAG-ASN : bond 0.00260 ( 14) link_NAG-ASN : angle 2.10550 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.678 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 REVERT: A 38 THR cc_start: 0.9034 (m) cc_final: 0.8776 (p) REVERT: A 247 ASP cc_start: 0.8499 (m-30) cc_final: 0.8014 (t0) REVERT: A 254 PHE cc_start: 0.8823 (t80) cc_final: 0.8493 (t80) REVERT: A 433 LEU cc_start: 0.9281 (mt) cc_final: 0.9012 (mt) REVERT: A 436 LEU cc_start: 0.9205 (pp) cc_final: 0.8628 (mt) REVERT: B 42 ASP cc_start: 0.8173 (t70) cc_final: 0.7889 (t0) REVERT: B 254 PHE cc_start: 0.9211 (t80) cc_final: 0.8903 (t80) REVERT: B 305 VAL cc_start: 0.9426 (t) cc_final: 0.9146 (m) REVERT: C 210 MET cc_start: 0.8493 (ppp) cc_final: 0.8180 (ppp) REVERT: C 221 LEU cc_start: 0.8294 (mm) cc_final: 0.7582 (tp) REVERT: C 254 PHE cc_start: 0.8916 (t80) cc_final: 0.8359 (t80) REVERT: D 197 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8581 (tmtt) REVERT: D 254 PHE cc_start: 0.8832 (t80) cc_final: 0.8448 (t80) REVERT: D 331 TRP cc_start: 0.5230 (m100) cc_final: 0.4567 (m100) REVERT: E 247 ASP cc_start: 0.8432 (m-30) cc_final: 0.7973 (t0) REVERT: E 259 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9017 (tp) REVERT: E 436 LEU cc_start: 0.9251 (pp) cc_final: 0.8823 (mt) outliers start: 13 outliers final: 1 residues processed: 218 average time/residue: 0.1154 time to fit residues: 40.7483 Evaluate side-chains 146 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 23 optimal weight: 0.0010 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 HIS E 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065035 restraints weight = 63370.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066948 restraints weight = 37092.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067836 restraints weight = 25841.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.068636 restraints weight = 21129.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068958 restraints weight = 18313.461| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17377 Z= 0.119 Angle : 0.745 10.766 23775 Z= 0.346 Chirality : 0.048 0.320 2819 Planarity : 0.004 0.043 2872 Dihedral : 11.778 172.283 2958 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.50 % Allowed : 4.36 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.19), residues: 1975 helix: 0.55 (0.20), residues: 730 sheet: -1.90 (0.28), residues: 325 loop : -2.89 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 120 TYR 0.030 0.001 TYR A 262 PHE 0.014 0.001 PHE E 412 TRP 0.014 0.001 TRP C 68 HIS 0.006 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00260 (17338) covalent geometry : angle 0.72896 (23675) SS BOND : bond 0.00650 ( 5) SS BOND : angle 0.93895 ( 10) hydrogen bonds : bond 0.03884 ( 648) hydrogen bonds : angle 4.43721 ( 1947) Misc. bond : bond 0.00457 ( 4) link_BETA1-3 : bond 0.00721 ( 2) link_BETA1-3 : angle 3.25891 ( 6) link_BETA1-4 : bond 0.00707 ( 14) link_BETA1-4 : angle 3.03424 ( 42) link_NAG-ASN : bond 0.00252 ( 14) link_NAG-ASN : angle 2.01125 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.688 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 REVERT: A 38 THR cc_start: 0.9020 (m) cc_final: 0.8753 (p) REVERT: A 247 ASP cc_start: 0.8586 (m-30) cc_final: 0.8037 (t0) REVERT: A 254 PHE cc_start: 0.8784 (t80) cc_final: 0.8449 (t80) REVERT: A 296 ILE cc_start: 0.9270 (pt) cc_final: 0.9044 (tt) REVERT: A 302 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9357 (tt) REVERT: A 433 LEU cc_start: 0.9310 (mt) cc_final: 0.9025 (mt) REVERT: A 436 LEU cc_start: 0.9194 (pp) cc_final: 0.8633 (mt) REVERT: B 42 ASP cc_start: 0.8196 (t70) cc_final: 0.7837 (t0) REVERT: B 210 MET cc_start: 0.8576 (tmm) cc_final: 0.8180 (tmm) REVERT: B 254 PHE cc_start: 0.9150 (t80) cc_final: 0.8813 (t80) REVERT: C 210 MET cc_start: 0.8364 (ppp) cc_final: 0.8164 (ppp) REVERT: C 221 LEU cc_start: 0.8276 (mm) cc_final: 0.7524 (tp) REVERT: C 254 PHE cc_start: 0.8727 (t80) cc_final: 0.8494 (t80) REVERT: C 291 MET cc_start: 0.8051 (mmp) cc_final: 0.7848 (mmp) REVERT: C 305 VAL cc_start: 0.9447 (t) cc_final: 0.9209 (m) REVERT: D 197 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8131 (tmtt) REVERT: D 254 PHE cc_start: 0.8852 (t80) cc_final: 0.8463 (t80) REVERT: D 331 TRP cc_start: 0.5641 (m100) cc_final: 0.4926 (m100) REVERT: E 64 TYR cc_start: 0.8819 (t80) cc_final: 0.8585 (t80) REVERT: E 247 ASP cc_start: 0.8521 (m-30) cc_final: 0.8032 (t0) REVERT: E 259 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9024 (tp) REVERT: E 305 VAL cc_start: 0.9373 (t) cc_final: 0.9127 (m) REVERT: E 436 LEU cc_start: 0.9246 (pp) cc_final: 0.8856 (mt) outliers start: 9 outliers final: 0 residues processed: 208 average time/residue: 0.1154 time to fit residues: 38.9857 Evaluate side-chains 147 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 79 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064826 restraints weight = 62548.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066518 restraints weight = 37412.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067724 restraints weight = 26564.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068249 restraints weight = 20994.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068702 restraints weight = 18537.056| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17377 Z= 0.119 Angle : 0.737 11.219 23775 Z= 0.340 Chirality : 0.047 0.319 2819 Planarity : 0.004 0.043 2872 Dihedral : 10.970 171.044 2958 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -1.84 (0.19), residues: 1975 helix: 0.73 (0.20), residues: 730 sheet: -1.69 (0.29), residues: 325 loop : -2.76 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 120 TYR 0.027 0.001 TYR A 262 PHE 0.015 0.001 PHE D 233 TRP 0.012 0.001 TRP C 68 HIS 0.004 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00269 (17338) covalent geometry : angle 0.72102 (23675) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.47735 ( 10) hydrogen bonds : bond 0.03861 ( 648) hydrogen bonds : angle 4.37853 ( 1947) Misc. bond : bond 0.00466 ( 4) link_BETA1-3 : bond 0.00652 ( 2) link_BETA1-3 : angle 3.07241 ( 6) link_BETA1-4 : bond 0.00717 ( 14) link_BETA1-4 : angle 2.96318 ( 42) link_NAG-ASN : bond 0.00233 ( 14) link_NAG-ASN : angle 1.99985 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.683 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: A 38 THR cc_start: 0.9047 (m) cc_final: 0.8782 (p) REVERT: A 247 ASP cc_start: 0.8553 (m-30) cc_final: 0.8004 (t0) REVERT: A 254 PHE cc_start: 0.8760 (t80) cc_final: 0.8407 (t80) REVERT: A 296 ILE cc_start: 0.9303 (pt) cc_final: 0.9069 (tt) REVERT: A 302 ILE cc_start: 0.9718 (mp) cc_final: 0.9380 (tt) REVERT: B 42 ASP cc_start: 0.8180 (t70) cc_final: 0.7844 (t0) REVERT: B 210 MET cc_start: 0.8572 (tmm) cc_final: 0.8100 (tmm) REVERT: B 254 PHE cc_start: 0.9085 (t80) cc_final: 0.8799 (t80) REVERT: C 221 LEU cc_start: 0.8299 (mm) cc_final: 0.7529 (tp) REVERT: C 254 PHE cc_start: 0.8690 (t80) cc_final: 0.8446 (t80) REVERT: C 266 LEU cc_start: 0.9207 (mt) cc_final: 0.8373 (pp) REVERT: C 417 ASP cc_start: 0.8135 (m-30) cc_final: 0.7803 (m-30) REVERT: D 197 LYS cc_start: 0.8460 (tmmt) cc_final: 0.7990 (tmtt) REVERT: D 254 PHE cc_start: 0.8830 (t80) cc_final: 0.8420 (t80) REVERT: D 331 TRP cc_start: 0.5789 (m100) cc_final: 0.4971 (m100) REVERT: E 64 TYR cc_start: 0.8796 (t80) cc_final: 0.8534 (t80) REVERT: E 247 ASP cc_start: 0.8522 (m-30) cc_final: 0.8030 (t0) REVERT: E 259 LEU cc_start: 0.9432 (pt) cc_final: 0.9072 (tp) REVERT: E 305 VAL cc_start: 0.9357 (t) cc_final: 0.9119 (m) REVERT: E 436 LEU cc_start: 0.9207 (pp) cc_final: 0.8852 (mt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1159 time to fit residues: 38.1339 Evaluate side-chains 138 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 154 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 124 optimal weight: 0.0870 chunk 32 optimal weight: 0.0170 chunk 128 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS E 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.084764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065300 restraints weight = 62751.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066996 restraints weight = 38184.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067956 restraints weight = 27169.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068782 restraints weight = 22130.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069028 restraints weight = 19016.089| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17377 Z= 0.114 Angle : 0.760 12.124 23775 Z= 0.346 Chirality : 0.047 0.314 2819 Planarity : 0.004 0.041 2872 Dihedral : 10.444 169.635 2958 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.66 (0.19), residues: 1975 helix: 0.84 (0.20), residues: 730 sheet: -1.48 (0.29), residues: 325 loop : -2.67 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 28 TYR 0.028 0.001 TYR A 262 PHE 0.014 0.001 PHE C 233 TRP 0.012 0.001 TRP C 68 HIS 0.006 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00255 (17338) covalent geometry : angle 0.74676 (23675) SS BOND : bond 0.00134 ( 5) SS BOND : angle 0.38863 ( 10) hydrogen bonds : bond 0.03815 ( 648) hydrogen bonds : angle 4.29334 ( 1947) Misc. bond : bond 0.00461 ( 4) link_BETA1-3 : bond 0.00622 ( 2) link_BETA1-3 : angle 2.78403 ( 6) link_BETA1-4 : bond 0.00663 ( 14) link_BETA1-4 : angle 2.82261 ( 42) link_NAG-ASN : bond 0.00228 ( 14) link_NAG-ASN : angle 1.95898 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.708 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 REVERT: A 38 THR cc_start: 0.9004 (m) cc_final: 0.8713 (p) REVERT: A 100 ILE cc_start: 0.8866 (pt) cc_final: 0.8593 (pt) REVERT: A 247 ASP cc_start: 0.8474 (m-30) cc_final: 0.7999 (t0) REVERT: A 254 PHE cc_start: 0.8721 (t80) cc_final: 0.8394 (t80) REVERT: A 296 ILE cc_start: 0.9312 (pt) cc_final: 0.9063 (tt) REVERT: A 302 ILE cc_start: 0.9702 (mp) cc_final: 0.9375 (tt) REVERT: B 42 ASP cc_start: 0.8086 (t70) cc_final: 0.7793 (t0) REVERT: B 210 MET cc_start: 0.8525 (tmm) cc_final: 0.8263 (tmm) REVERT: C 221 LEU cc_start: 0.8339 (mm) cc_final: 0.7591 (tp) REVERT: C 254 PHE cc_start: 0.8645 (t80) cc_final: 0.8406 (t80) REVERT: C 266 LEU cc_start: 0.8996 (mt) cc_final: 0.8335 (pp) REVERT: C 417 ASP cc_start: 0.8090 (m-30) cc_final: 0.7794 (m-30) REVERT: D 254 PHE cc_start: 0.8790 (t80) cc_final: 0.8403 (t80) REVERT: D 331 TRP cc_start: 0.5694 (m100) cc_final: 0.4753 (m100) REVERT: E 247 ASP cc_start: 0.8438 (m-30) cc_final: 0.7965 (t0) REVERT: E 259 LEU cc_start: 0.9377 (pt) cc_final: 0.9056 (tp) REVERT: E 305 VAL cc_start: 0.9325 (t) cc_final: 0.9106 (m) REVERT: E 436 LEU cc_start: 0.9184 (pp) cc_final: 0.8857 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1093 time to fit residues: 37.0133 Evaluate side-chains 145 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 47 optimal weight: 0.0570 chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.083788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064049 restraints weight = 62947.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065775 restraints weight = 37923.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066865 restraints weight = 26853.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067719 restraints weight = 21385.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067988 restraints weight = 18293.179| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17377 Z= 0.124 Angle : 0.758 12.834 23775 Z= 0.349 Chirality : 0.047 0.313 2819 Planarity : 0.004 0.042 2872 Dihedral : 10.122 166.795 2958 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: -1.50 (0.19), residues: 1975 helix: 0.96 (0.20), residues: 730 sheet: -1.41 (0.30), residues: 325 loop : -2.55 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.030 0.001 TYR A 262 PHE 0.015 0.001 PHE E 233 TRP 0.012 0.001 TRP C 68 HIS 0.012 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00280 (17338) covalent geometry : angle 0.74540 (23675) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.53159 ( 10) hydrogen bonds : bond 0.03828 ( 648) hydrogen bonds : angle 4.31280 ( 1947) Misc. bond : bond 0.00452 ( 4) link_BETA1-3 : bond 0.00645 ( 2) link_BETA1-3 : angle 2.41566 ( 6) link_BETA1-4 : bond 0.00713 ( 14) link_BETA1-4 : angle 2.66837 ( 42) link_NAG-ASN : bond 0.00199 ( 14) link_NAG-ASN : angle 2.03375 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.619 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 REVERT: A 38 THR cc_start: 0.9117 (m) cc_final: 0.8850 (p) REVERT: A 247 ASP cc_start: 0.8634 (m-30) cc_final: 0.8141 (t0) REVERT: A 254 PHE cc_start: 0.8788 (t80) cc_final: 0.8468 (t80) REVERT: A 296 ILE cc_start: 0.9320 (pt) cc_final: 0.9073 (tt) REVERT: A 302 ILE cc_start: 0.9702 (mp) cc_final: 0.9354 (tt) REVERT: B 42 ASP cc_start: 0.8228 (t70) cc_final: 0.7916 (t0) REVERT: B 210 MET cc_start: 0.8600 (tmm) cc_final: 0.8211 (tmm) REVERT: B 254 PHE cc_start: 0.9274 (t80) cc_final: 0.8922 (t80) REVERT: B 258 LEU cc_start: 0.9742 (pt) cc_final: 0.9516 (pt) REVERT: B 436 LEU cc_start: 0.9227 (pp) cc_final: 0.8959 (mm) REVERT: C 221 LEU cc_start: 0.8364 (mm) cc_final: 0.7583 (tp) REVERT: C 254 PHE cc_start: 0.8709 (t80) cc_final: 0.8484 (t80) REVERT: C 417 ASP cc_start: 0.8194 (m-30) cc_final: 0.7901 (m-30) REVERT: D 254 PHE cc_start: 0.8857 (t80) cc_final: 0.8482 (t80) REVERT: D 302 ILE cc_start: 0.9675 (mp) cc_final: 0.9355 (tt) REVERT: D 331 TRP cc_start: 0.5662 (m100) cc_final: 0.4699 (m100) REVERT: E 247 ASP cc_start: 0.8529 (m-30) cc_final: 0.8016 (t0) REVERT: E 259 LEU cc_start: 0.9397 (pt) cc_final: 0.9101 (tp) REVERT: E 305 VAL cc_start: 0.9350 (t) cc_final: 0.9136 (m) REVERT: E 436 LEU cc_start: 0.9223 (pp) cc_final: 0.8938 (mt) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0987 time to fit residues: 32.8416 Evaluate side-chains 140 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 172 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060867 restraints weight = 65020.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062559 restraints weight = 40308.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063750 restraints weight = 28763.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064240 restraints weight = 22894.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064701 restraints weight = 20404.187| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17377 Z= 0.157 Angle : 0.792 12.759 23775 Z= 0.371 Chirality : 0.048 0.315 2819 Planarity : 0.004 0.039 2872 Dihedral : 9.865 163.566 2958 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1975 helix: 0.99 (0.20), residues: 730 sheet: -1.42 (0.30), residues: 325 loop : -2.45 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.039 0.002 TYR A 262 PHE 0.017 0.002 PHE B 233 TRP 0.015 0.001 TRP C 168 HIS 0.006 0.001 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00362 (17338) covalent geometry : angle 0.78037 (23675) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.64602 ( 10) hydrogen bonds : bond 0.03964 ( 648) hydrogen bonds : angle 4.33522 ( 1947) Misc. bond : bond 0.00449 ( 4) link_BETA1-3 : bond 0.00670 ( 2) link_BETA1-3 : angle 2.19111 ( 6) link_BETA1-4 : bond 0.00645 ( 14) link_BETA1-4 : angle 2.54430 ( 42) link_NAG-ASN : bond 0.00200 ( 14) link_NAG-ASN : angle 2.18783 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.704 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 38 THR cc_start: 0.9179 (m) cc_final: 0.8916 (p) REVERT: A 247 ASP cc_start: 0.8668 (m-30) cc_final: 0.8188 (t0) REVERT: A 296 ILE cc_start: 0.9385 (pt) cc_final: 0.9130 (tt) REVERT: A 302 ILE cc_start: 0.9710 (mp) cc_final: 0.9383 (tt) REVERT: B 210 MET cc_start: 0.8613 (tmm) cc_final: 0.8249 (tmm) REVERT: B 254 PHE cc_start: 0.9307 (t80) cc_final: 0.8969 (t80) REVERT: B 436 LEU cc_start: 0.9234 (pp) cc_final: 0.8959 (mm) REVERT: C 221 LEU cc_start: 0.8435 (mm) cc_final: 0.7621 (tp) REVERT: C 254 PHE cc_start: 0.8786 (t80) cc_final: 0.8539 (t80) REVERT: C 417 ASP cc_start: 0.8210 (m-30) cc_final: 0.7878 (m-30) REVERT: D 197 LYS cc_start: 0.8397 (tmmt) cc_final: 0.7964 (tmtt) REVERT: D 302 ILE cc_start: 0.9682 (mp) cc_final: 0.9346 (tt) REVERT: D 331 TRP cc_start: 0.5621 (m100) cc_final: 0.4526 (m100) REVERT: E 247 ASP cc_start: 0.8582 (m-30) cc_final: 0.8062 (t0) REVERT: E 259 LEU cc_start: 0.9387 (pt) cc_final: 0.9063 (tp) REVERT: E 305 VAL cc_start: 0.9400 (t) cc_final: 0.9173 (m) REVERT: E 436 LEU cc_start: 0.9279 (pp) cc_final: 0.8973 (mt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1101 time to fit residues: 34.3745 Evaluate side-chains 126 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 167 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.061527 restraints weight = 64134.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063348 restraints weight = 39348.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064468 restraints weight = 27802.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065317 restraints weight = 22110.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065600 restraints weight = 19009.101| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17377 Z= 0.125 Angle : 0.793 14.561 23775 Z= 0.363 Chirality : 0.047 0.310 2819 Planarity : 0.004 0.040 2872 Dihedral : 9.336 163.390 2958 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -1.34 (0.20), residues: 1975 helix: 1.03 (0.20), residues: 730 sheet: -1.32 (0.30), residues: 325 loop : -2.39 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.033 0.001 TYR A 262 PHE 0.030 0.001 PHE E 233 TRP 0.010 0.001 TRP C 68 HIS 0.002 0.000 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00286 (17338) covalent geometry : angle 0.78140 (23675) SS BOND : bond 0.00106 ( 5) SS BOND : angle 0.52993 ( 10) hydrogen bonds : bond 0.03911 ( 648) hydrogen bonds : angle 4.25959 ( 1947) Misc. bond : bond 0.00454 ( 4) link_BETA1-3 : bond 0.00656 ( 2) link_BETA1-3 : angle 2.11978 ( 6) link_BETA1-4 : bond 0.00655 ( 14) link_BETA1-4 : angle 2.53283 ( 42) link_NAG-ASN : bond 0.00181 ( 14) link_NAG-ASN : angle 2.06011 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.670 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 38 THR cc_start: 0.9167 (m) cc_final: 0.8896 (p) REVERT: A 247 ASP cc_start: 0.8682 (m-30) cc_final: 0.8215 (t0) REVERT: A 254 PHE cc_start: 0.8845 (t80) cc_final: 0.8531 (t80) REVERT: A 296 ILE cc_start: 0.9334 (pt) cc_final: 0.9089 (tt) REVERT: A 302 ILE cc_start: 0.9682 (mp) cc_final: 0.9301 (tt) REVERT: B 210 MET cc_start: 0.8535 (tmm) cc_final: 0.8032 (tmm) REVERT: B 436 LEU cc_start: 0.9240 (pp) cc_final: 0.8968 (mm) REVERT: C 221 LEU cc_start: 0.8439 (mm) cc_final: 0.7605 (tp) REVERT: C 254 PHE cc_start: 0.8735 (t80) cc_final: 0.8487 (t80) REVERT: C 417 ASP cc_start: 0.8259 (m-30) cc_final: 0.7978 (m-30) REVERT: D 197 LYS cc_start: 0.8248 (tmmt) cc_final: 0.7818 (tmtt) REVERT: D 302 ILE cc_start: 0.9674 (mp) cc_final: 0.9327 (tt) REVERT: D 331 TRP cc_start: 0.5656 (m100) cc_final: 0.4513 (m100) REVERT: E 229 LEU cc_start: 0.9095 (pt) cc_final: 0.8604 (tt) REVERT: E 247 ASP cc_start: 0.8591 (m-30) cc_final: 0.8068 (t0) REVERT: E 305 VAL cc_start: 0.9389 (t) cc_final: 0.9130 (m) REVERT: E 436 LEU cc_start: 0.9238 (pp) cc_final: 0.8957 (mt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1060 time to fit residues: 32.6358 Evaluate side-chains 124 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 132 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 130 optimal weight: 3.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061743 restraints weight = 63624.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063367 restraints weight = 40402.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064484 restraints weight = 29320.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064935 restraints weight = 23660.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065454 restraints weight = 21177.274| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17377 Z= 0.126 Angle : 0.798 13.903 23775 Z= 0.365 Chirality : 0.047 0.308 2819 Planarity : 0.004 0.040 2872 Dihedral : 9.093 163.175 2958 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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 (0.20), residues: 1975 helix: 1.01 (0.20), residues: 730 sheet: -1.51 (0.28), residues: 355 loop : -2.27 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.036 0.001 TYR A 262 PHE 0.020 0.001 PHE E 233 TRP 0.010 0.001 TRP A 331 HIS 0.002 0.000 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00289 (17338) covalent geometry : angle 0.78726 (23675) SS BOND : bond 0.00116 ( 5) SS BOND : angle 0.61271 ( 10) hydrogen bonds : bond 0.03941 ( 648) hydrogen bonds : angle 4.29344 ( 1947) Misc. bond : bond 0.00451 ( 4) link_BETA1-3 : bond 0.00604 ( 2) link_BETA1-3 : angle 1.82913 ( 6) link_BETA1-4 : bond 0.00655 ( 14) link_BETA1-4 : angle 2.49181 ( 42) link_NAG-ASN : bond 0.00188 ( 14) link_NAG-ASN : angle 2.06374 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.719 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: A 38 THR cc_start: 0.9175 (m) cc_final: 0.8934 (p) REVERT: A 247 ASP cc_start: 0.8807 (m-30) cc_final: 0.8231 (t0) REVERT: A 254 PHE cc_start: 0.8846 (t80) cc_final: 0.8555 (t80) REVERT: A 296 ILE cc_start: 0.9346 (pt) cc_final: 0.9124 (tt) REVERT: A 302 ILE cc_start: 0.9664 (mp) cc_final: 0.9355 (tt) REVERT: B 210 MET cc_start: 0.8579 (tmm) cc_final: 0.8106 (tmm) REVERT: B 436 LEU cc_start: 0.9172 (pp) cc_final: 0.8847 (mm) REVERT: C 221 LEU cc_start: 0.8440 (mm) cc_final: 0.7609 (tp) REVERT: C 254 PHE cc_start: 0.8712 (t80) cc_final: 0.8468 (t80) REVERT: C 436 LEU cc_start: 0.9168 (pp) cc_final: 0.8618 (mt) REVERT: D 197 LYS cc_start: 0.8260 (tmmt) cc_final: 0.7793 (tmtt) REVERT: D 302 ILE cc_start: 0.9678 (mp) cc_final: 0.9324 (tt) REVERT: D 331 TRP cc_start: 0.5615 (m100) cc_final: 0.4468 (m100) REVERT: E 229 LEU cc_start: 0.9134 (pt) cc_final: 0.8764 (tt) REVERT: E 247 ASP cc_start: 0.8616 (m-30) cc_final: 0.8117 (t0) REVERT: E 436 LEU cc_start: 0.9246 (pp) cc_final: 0.8973 (mt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1062 time to fit residues: 30.7546 Evaluate side-chains 123 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 127 optimal weight: 0.0770 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 125 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.081961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062054 restraints weight = 63966.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.063774 restraints weight = 38604.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064977 restraints weight = 27662.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.065448 restraints weight = 21960.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065924 restraints weight = 19649.238| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17377 Z= 0.117 Angle : 0.788 15.157 23775 Z= 0.356 Chirality : 0.047 0.305 2819 Planarity : 0.004 0.040 2872 Dihedral : 8.853 163.275 2958 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.27 (0.20), residues: 1975 helix: 1.04 (0.20), residues: 730 sheet: -1.41 (0.29), residues: 355 loop : -2.26 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.035 0.001 TYR A 262 PHE 0.023 0.001 PHE E 233 TRP 0.011 0.001 TRP A 331 HIS 0.002 0.000 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00270 (17338) covalent geometry : angle 0.77744 (23675) SS BOND : bond 0.00066 ( 5) SS BOND : angle 0.54020 ( 10) hydrogen bonds : bond 0.03820 ( 648) hydrogen bonds : angle 4.22126 ( 1947) Misc. bond : bond 0.00452 ( 4) link_BETA1-3 : bond 0.00587 ( 2) link_BETA1-3 : angle 1.87130 ( 6) link_BETA1-4 : bond 0.00664 ( 14) link_BETA1-4 : angle 2.46706 ( 42) link_NAG-ASN : bond 0.00190 ( 14) link_NAG-ASN : angle 2.01958 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.05 seconds wall clock time: 43 minutes 3.37 seconds (2583.37 seconds total)