Starting phenix.real_space_refine on Mon Sep 14 09:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.cif Found real_map, /net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.map" model { file = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6be1_7088/09_2026/6be1_7088.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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 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 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 49 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: 24 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: 25 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: 25 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: 4.11, per 1000 atoms: 0.24 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: 1.25 Conformation dependent library (CDL) restraints added in 718.0 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: 0.47 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: 3.11 Time building geometry restraints manager: 1.67 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 - 15.05: 9108 15.05 - 30.11: 574 30.11 - 45.16: 239 45.16 - 60.21: 12 60.21 - 75.27: 5 Dihedral angle restraints: 9938 sinusoidal: 3993 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 9935 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: 2.840 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.490 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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:1.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 11.552 75.267 6053 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/Z covalent geometry : bond 0.00644 / 0.33 (17338) covalent geometry : angle 1.27799 / 0.60 (23675) SS BOND : bond 0.00123 / 0.07 ( 5) SS BOND : angle 0.59815 / 0.35 ( 10) hydrogen bonds : bond 0.15541 / 10.32 ( 648) hydrogen bonds : angle 6.72392 / 4.61 ( 1947) Misc. bond : bond 0.00928 / 0.49 ( 4) link_BETA1-3 : bond 0.02440 / 1.16 ( 2) link_BETA1-3 : angle 11.43603 / 6.10 ( 6) link_BETA1-4 : bond 0.03232 / 1.99 ( 14) link_BETA1-4 : angle 13.57636 / 7.76 ( 42) link_NAG-ASN : bond 0.00385 / 0.22 ( 14) link_NAG-ASN : angle 2.69478 / 1.96 ( 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 : 0.581 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: 0.8404 (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: 0.7462 (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: 0.8894 (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: 0.1243 time to fit residues: 70.0925 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 : 0.695 ------------------------------------------------------------------------------- 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... ** 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 = 0.3561 r_free = 0.3561 target = 0.088082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068610 restraints weight = 63184.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070481 restraints weight = 36930.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071669 restraints weight = 26096.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072536 restraints weight = 20664.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072882 restraints weight = 17765.038| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2260 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= 0.156 Angle : 0.767 10.702 23775 Z= 0.368 Chirality : 0.049 0.346 2819 Planarity : 0.005 0.050 2872 Dihedral : 5.348 48.885 2222 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.66 % Allowed : 5.91 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.17), residues: 1975 helix: -0.39 (0.19), residues: 725 sheet: -2.33 (0.30), residues: 275 loop : -3.34 (0.16), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 416 TYR 0.023 0.001 TYR C 262 PHE 0.023 0.002 PHE D 412 TRP 0.018 0.001 TRP C 68 HIS 0.012 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (17338) covalent geometry : angle 0.74608 / 0.36 (23675) SS BOND : bond 0.01057 / 0.65 ( 5) SS BOND : angle 0.46661 / 0.22 ( 10) hydrogen bonds : bond 0.04505 / 2.93 ( 648) hydrogen bonds : angle 5.04425 / 3.50 ( 1947) Misc. bond : bond 0.00452 / 0.24 ( 4) link_BETA1-3 : bond 0.01318 / 0.63 ( 2) link_BETA1-3 : angle 3.08383 / 2.30 ( 6) link_BETA1-4 : bond 0.00982 / 0.58 ( 14) link_BETA1-4 : angle 3.57669 / 2.04 ( 42) link_NAG-ASN : bond 0.00270 / 0.17 ( 14) link_NAG-ASN : angle 2.19032 / 1.64 ( 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 268 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 0.625 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: 0.8996 (m) cc_final: 0.8756 (p) REVERT: A 247 ASP cc_start: 0.8446 (m-30) cc_final: 0.7905 (t0) REVERT: A 254 PHE cc_start: 0.8794 (t80) cc_final: 0.8448 (t80) REVERT: A 433 LEU cc_start: 0.9290 (mt) cc_final: 0.8997 (mt) REVERT: A 434 ASP cc_start: 0.8581 (t0) cc_final: 0.8347 (t70) REVERT: A 436 LEU cc_start: 0.9188 (pp) cc_final: 0.8568 (mt) REVERT: B 42 ASP cc_start: 0.8022 (t70) cc_final: 0.7755 (t0) REVERT: B 254 PHE cc_start: 0.9241 (t80) cc_final: 0.8946 (t80) REVERT: C 210 MET cc_start: 0.8270 (ppp) cc_final: 0.7890 (ppp) REVERT: C 221 LEU cc_start: 0.8210 (mm) cc_final: 0.7575 (tp) REVERT: C 254 PHE cc_start: 0.8840 (t80) cc_final: 0.8516 (t80) REVERT: C 305 VAL cc_start: 0.9462 (t) cc_final: 0.9230 (m) REVERT: D 210 MET cc_start: 0.8120 (ppp) cc_final: 0.7829 (ppp) REVERT: D 223 TYR cc_start: 0.6873 (p90) cc_final: 0.6668 (p90) REVERT: D 254 PHE cc_start: 0.9014 (t80) cc_final: 0.8310 (t80) REVERT: D 331 TRP cc_start: 0.5149 (m100) cc_final: 0.4572 (m100) REVERT: E 247 ASP cc_start: 0.8398 (m-30) cc_final: 0.7908 (t0) REVERT: E 259 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9027 (tp) REVERT: E 413 LEU cc_start: 0.9329 (mt) cc_final: 0.9004 (mt) outliers start: 12 outliers final: 0 residues processed: 260 average time/residue: 0.1184 time to fit residues: 48.6226 Evaluate side-chains 163 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 5.9990 chunk 180 optimal weight: 7.9990 chunk 188 optimal weight: 0.0030 chunk 157 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 165 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3562 r_free = 0.3562 target = 0.088089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069091 restraints weight = 63493.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070855 restraints weight = 38524.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071906 restraints weight = 27641.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072743 restraints weight = 22213.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073051 restraints weight = 19224.420| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17377 Z= 0.116 Angle : 0.731 11.291 23775 Z= 0.342 Chirality : 0.048 0.309 2819 Planarity : 0.005 0.051 2872 Dihedral : 5.048 45.797 2222 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.55 % Allowed : 5.02 % Favored : 94.42 % 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: -2.55 (0.18), residues: 1975 helix: 0.15 (0.20), residues: 725 sheet: -2.01 (0.28), residues: 325 loop : -3.19 (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 0.015 0.001 PHE A 233 TRP 0.015 0.001 TRP C 68 HIS 0.003 0.001 HIS C 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17338) covalent geometry : angle 0.71739 / 0.34 (23675) SS BOND : bond 0.00085 / 0.05 ( 5) SS BOND : angle 0.50610 / 0.26 ( 10) hydrogen bonds : bond 0.04088 / 2.65 ( 648) hydrogen bonds : angle 4.67161 / 3.25 ( 1947) Misc. bond : bond 0.00408 / 0.21 ( 4) link_BETA1-3 : bond 0.00509 / 0.24 ( 2) link_BETA1-3 : angle 2.32105 / 1.61 ( 6) link_BETA1-4 : bond 0.00815 / 0.49 ( 14) link_BETA1-4 : angle 2.80268 / 1.60 ( 42) link_NAG-ASN : bond 0.00293 / 0.16 ( 14) link_NAG-ASN : angle 2.00012 / 1.53 ( 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 240 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.611 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: 0.8862 (m) cc_final: 0.8569 (p) REVERT: A 247 ASP cc_start: 0.8282 (m-30) cc_final: 0.7868 (t0) REVERT: A 254 PHE cc_start: 0.8690 (t80) cc_final: 0.8375 (t80) REVERT: A 433 LEU cc_start: 0.9218 (mt) cc_final: 0.8962 (mt) REVERT: A 436 LEU cc_start: 0.9139 (pp) cc_final: 0.8518 (mt) REVERT: B 254 PHE cc_start: 0.9076 (t80) cc_final: 0.8866 (t80) REVERT: B 305 VAL cc_start: 0.9391 (t) cc_final: 0.9150 (m) REVERT: C 221 LEU cc_start: 0.8186 (mm) cc_final: 0.7512 (tp) REVERT: C 254 PHE cc_start: 0.8759 (t80) cc_final: 0.8509 (t80) REVERT: C 305 VAL cc_start: 0.9383 (t) cc_final: 0.9180 (m) REVERT: D 197 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8540 (tmtt) REVERT: D 254 PHE cc_start: 0.8682 (t80) cc_final: 0.8309 (t80) REVERT: D 331 TRP cc_start: 0.5126 (m100) cc_final: 0.4482 (m100) REVERT: E 247 ASP cc_start: 0.8256 (m-30) cc_final: 0.7854 (t0) REVERT: E 254 PHE cc_start: 0.9096 (t80) cc_final: 0.8786 (t80) REVERT: E 259 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8955 (tp) REVERT: E 428 ARG cc_start: 0.9139 (tpt170) cc_final: 0.8896 (tpp80) REVERT: E 436 LEU cc_start: 0.9202 (pp) cc_final: 0.8743 (mt) outliers start: 10 outliers final: 1 residues processed: 233 average time/residue: 0.1083 time to fit residues: 40.4005 Evaluate side-chains 158 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 0.8980 chunk 170 optimal weight: 3.9990 chunk 23 optimal weight: 0.0000 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 119 HIS B 460 HIS D 55 ASN E 55 ASN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.080829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.061108 restraints weight = 64624.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063043 restraints weight = 38558.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063168 restraints weight = 25865.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063413 restraints weight = 24243.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063607 restraints weight = 22706.955| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17377 Z= 0.205 Angle : 0.772 10.873 23775 Z= 0.383 Chirality : 0.049 0.347 2819 Planarity : 0.005 0.050 2872 Dihedral : 5.208 39.368 2222 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.44 % Allowed : 5.02 % 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: -2.17 (0.18), residues: 1975 helix: 0.44 (0.20), residues: 730 sheet: -2.17 (0.28), residues: 325 loop : -2.80 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 251 TYR 0.030 0.002 TYR A 262 PHE 0.045 0.002 PHE C 412 TRP 0.022 0.002 TRP D 168 HIS 0.007 0.002 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (17338) covalent geometry : angle 0.75992 / 0.38 (23675) SS BOND : bond 0.00244 / 0.14 ( 5) SS BOND : angle 1.29238 / 0.74 ( 10) hydrogen bonds : bond 0.04450 / 2.91 ( 648) hydrogen bonds : angle 4.63080 / 3.22 ( 1947) Misc. bond : bond 0.00357 / 0.19 ( 4) link_BETA1-3 : bond 0.00728 / 0.35 ( 2) link_BETA1-3 : angle 2.04666 / 1.37 ( 6) link_BETA1-4 : bond 0.00732 / 0.44 ( 14) link_BETA1-4 : angle 2.33748 / 1.40 ( 42) link_NAG-ASN : bond 0.00303 / 0.16 ( 14) link_NAG-ASN : angle 2.40937 / 1.96 ( 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 207 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.634 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: 0.9214 (m) cc_final: 0.8950 (p) REVERT: A 247 ASP cc_start: 0.8690 (m-30) cc_final: 0.8087 (t0) REVERT: A 254 PHE cc_start: 0.8980 (t80) cc_final: 0.8658 (t80) REVERT: B 210 MET cc_start: 0.8604 (tmm) cc_final: 0.8142 (tmm) REVERT: B 436 LEU cc_start: 0.9135 (pp) cc_final: 0.8766 (mm) REVERT: C 210 MET cc_start: 0.8712 (ppp) cc_final: 0.8445 (ppp) REVERT: C 221 LEU cc_start: 0.8362 (mm) cc_final: 0.7571 (tp) REVERT: C 254 PHE cc_start: 0.9032 (t80) cc_final: 0.8433 (t80) REVERT: C 417 ASP cc_start: 0.8329 (m-30) cc_final: 0.7900 (m-30) REVERT: D 254 PHE cc_start: 0.8992 (t80) cc_final: 0.8612 (t80) REVERT: D 331 TRP cc_start: 0.5580 (m100) cc_final: 0.4863 (m100) REVERT: E 247 ASP cc_start: 0.8624 (m-30) cc_final: 0.8073 (t0) REVERT: E 259 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.8972 (tp) REVERT: E 305 VAL cc_start: 0.9441 (t) cc_final: 0.9209 (m) REVERT: E 436 LEU cc_start: 0.9316 (pp) cc_final: 0.8903 (mt) outliers start: 8 outliers final: 0 residues processed: 201 average time/residue: 0.1004 time to fit residues: 33.5544 Evaluate side-chains 129 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 0.8980 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** 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 = 0.3450 r_free = 0.3450 target = 0.082469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062715 restraints weight = 62702.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064390 restraints weight = 38399.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065297 restraints weight = 27638.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066086 restraints weight = 22723.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066455 restraints weight = 19623.142| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3805 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= 0.121 Angle : 0.737 11.190 23775 Z= 0.346 Chirality : 0.047 0.321 2819 Planarity : 0.004 0.043 2872 Dihedral : 4.985 38.298 2222 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -1.85 (0.19), residues: 1975 helix: 0.74 (0.20), residues: 730 sheet: -1.85 (0.29), residues: 325 loop : -2.70 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 416 TYR 0.029 0.001 TYR A 262 PHE 0.033 0.002 PHE C 412 TRP 0.012 0.001 TRP A 68 HIS 0.003 0.001 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17338) covalent geometry : angle 0.72649 / 0.34 (23675) SS BOND : bond 0.00105 / 0.06 ( 5) SS BOND : angle 0.93102 / 0.52 ( 10) hydrogen bonds : bond 0.04014 / 2.61 ( 648) hydrogen bonds : angle 4.38379 / 3.05 ( 1947) Misc. bond : bond 0.00366 / 0.19 ( 4) link_BETA1-3 : bond 0.00577 / 0.27 ( 2) link_BETA1-3 : angle 1.97426 / 1.35 ( 6) link_BETA1-4 : bond 0.00707 / 0.43 ( 14) link_BETA1-4 : angle 2.26904 / 1.34 ( 42) link_NAG-ASN : bond 0.00189 / 0.11 ( 14) link_NAG-ASN : angle 2.02187 / 1.62 ( 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 199 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9146 (m) cc_final: 0.8852 (p) REVERT: A 247 ASP cc_start: 0.8597 (m-30) cc_final: 0.8038 (t0) REVERT: A 254 PHE cc_start: 0.8909 (t80) cc_final: 0.8541 (t80) REVERT: A 302 ILE cc_start: 0.9783 (mt) cc_final: 0.9511 (tp) REVERT: B 42 ASP cc_start: 0.8301 (t70) cc_final: 0.8023 (t0) REVERT: B 210 MET cc_start: 0.8586 (tmm) cc_final: 0.8287 (tmm) REVERT: C 221 LEU cc_start: 0.8232 (mm) cc_final: 0.7439 (tp) REVERT: C 254 PHE cc_start: 0.8808 (t80) cc_final: 0.8512 (t80) REVERT: C 266 LEU cc_start: 0.9216 (mt) cc_final: 0.9013 (mt) REVERT: D 254 PHE cc_start: 0.8935 (t80) cc_final: 0.8518 (t80) REVERT: D 331 TRP cc_start: 0.5598 (m100) cc_final: 0.4784 (m100) REVERT: E 247 ASP cc_start: 0.8589 (m-30) cc_final: 0.8063 (t0) REVERT: E 259 LEU cc_start: 0.9419 (pt) cc_final: 0.9061 (tp) REVERT: E 436 LEU cc_start: 0.9298 (pp) cc_final: 0.8906 (mt) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.0962 time to fit residues: 32.4648 Evaluate side-chains 134 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 177 optimal weight: 0.0670 chunk 131 optimal weight: 7.9990 chunk 24 optimal weight: 0.0270 chunk 172 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS D 55 ASN E 411 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062429 restraints weight = 63299.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064146 restraints weight = 38490.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065287 restraints weight = 27218.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065765 restraints weight = 21572.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066417 restraints weight = 19332.348| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17377 Z= 0.120 Angle : 0.742 11.304 23775 Z= 0.348 Chirality : 0.047 0.329 2819 Planarity : 0.004 0.041 2872 Dihedral : 4.854 36.711 2222 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 0.85 (0.20), residues: 730 sheet: -1.70 (0.29), residues: 325 loop : -2.59 (0.19), 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 0.023 0.001 PHE E 412 TRP 0.011 0.001 TRP C 68 HIS 0.003 0.000 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17338) covalent geometry : angle 0.73223 / 0.35 (23675) SS BOND : bond 0.00168 / 0.10 ( 5) SS BOND : angle 0.81229 / 0.46 ( 10) hydrogen bonds : bond 0.03978 / 2.59 ( 648) hydrogen bonds : angle 4.35766 / 3.04 ( 1947) Misc. bond : bond 0.00356 / 0.19 ( 4) link_BETA1-3 : bond 0.00580 / 0.28 ( 2) link_BETA1-3 : angle 1.83958 / 1.25 ( 6) link_BETA1-4 : bond 0.00707 / 0.43 ( 14) link_BETA1-4 : angle 2.25662 / 1.34 ( 42) link_NAG-ASN : bond 0.00201 / 0.11 ( 14) link_NAG-ASN : angle 1.98589 / 1.59 ( 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 194 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9157 (m) cc_final: 0.8874 (p) REVERT: A 247 ASP cc_start: 0.8651 (m-30) cc_final: 0.8087 (t0) REVERT: A 254 PHE cc_start: 0.8868 (t80) cc_final: 0.8519 (t80) REVERT: A 302 ILE cc_start: 0.9779 (mt) cc_final: 0.9488 (tp) REVERT: B 42 ASP cc_start: 0.8270 (t70) cc_final: 0.8010 (t0) REVERT: B 210 MET cc_start: 0.8568 (tmm) cc_final: 0.8271 (tmm) REVERT: B 417 ASP cc_start: 0.8709 (t70) cc_final: 0.8499 (t70) REVERT: C 221 LEU cc_start: 0.8400 (mm) cc_final: 0.7590 (tp) REVERT: C 254 PHE cc_start: 0.8772 (t80) cc_final: 0.8490 (t80) REVERT: C 266 LEU cc_start: 0.9013 (mt) cc_final: 0.8366 (pp) REVERT: D 254 PHE cc_start: 0.8881 (t80) cc_final: 0.8471 (t80) REVERT: D 331 TRP cc_start: 0.5713 (m100) cc_final: 0.4774 (m100) REVERT: E 247 ASP cc_start: 0.8603 (m-30) cc_final: 0.8043 (t0) REVERT: E 259 LEU cc_start: 0.9407 (pt) cc_final: 0.9063 (tp) REVERT: E 305 VAL cc_start: 0.9404 (t) cc_final: 0.9182 (m) REVERT: E 436 LEU cc_start: 0.9247 (pp) cc_final: 0.8902 (mt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1030 time to fit residues: 32.9840 Evaluate side-chains 133 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 0.0970 chunk 110 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 0.2980 chunk 33 optimal weight: 0.0870 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 ASN E 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063295 restraints weight = 62765.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064991 restraints weight = 38842.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066126 restraints weight = 27640.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066849 restraints weight = 21936.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067047 restraints weight = 19126.957| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4011 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= 0.115 Angle : 0.760 12.657 23775 Z= 0.350 Chirality : 0.047 0.333 2819 Planarity : 0.004 0.041 2872 Dihedral : 4.749 34.727 2222 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -1.57 (0.19), residues: 1975 helix: 0.89 (0.20), residues: 730 sheet: -1.53 (0.30), residues: 325 loop : -2.54 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 28 TYR 0.030 0.001 TYR A 262 PHE 0.017 0.001 PHE E 412 TRP 0.012 0.001 TRP C 68 HIS 0.003 0.000 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17338) covalent geometry : angle 0.75084 / 0.35 (23675) SS BOND : bond 0.00087 / 0.05 ( 5) SS BOND : angle 0.69262 / 0.39 ( 10) hydrogen bonds : bond 0.03898 / 2.52 ( 648) hydrogen bonds : angle 4.29459 / 3.00 ( 1947) Misc. bond : bond 0.00345 / 0.18 ( 4) link_BETA1-3 : bond 0.00537 / 0.26 ( 2) link_BETA1-3 : angle 1.78749 / 1.23 ( 6) link_BETA1-4 : bond 0.00710 / 0.42 ( 14) link_BETA1-4 : angle 2.21288 / 1.32 ( 42) link_NAG-ASN : bond 0.00220 / 0.12 ( 14) link_NAG-ASN : angle 1.88935 / 1.50 ( 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 193 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9115 (m) cc_final: 0.8842 (p) REVERT: A 98 ILE cc_start: 0.9299 (mm) cc_final: 0.8985 (tp) REVERT: A 247 ASP cc_start: 0.8600 (m-30) cc_final: 0.8111 (t0) REVERT: A 254 PHE cc_start: 0.8781 (t80) cc_final: 0.8466 (t80) REVERT: A 302 ILE cc_start: 0.9777 (mt) cc_final: 0.9500 (tp) REVERT: B 42 ASP cc_start: 0.8213 (t70) cc_final: 0.7984 (t0) REVERT: B 210 MET cc_start: 0.8527 (tmm) cc_final: 0.8244 (tmm) REVERT: B 417 ASP cc_start: 0.8816 (t70) cc_final: 0.8457 (t70) REVERT: C 221 LEU cc_start: 0.8355 (mm) cc_final: 0.7543 (tp) REVERT: C 254 PHE cc_start: 0.8693 (t80) cc_final: 0.8442 (t80) REVERT: D 254 PHE cc_start: 0.8826 (t80) cc_final: 0.8460 (t80) REVERT: D 331 TRP cc_start: 0.5681 (m100) cc_final: 0.4583 (m100) REVERT: E 247 ASP cc_start: 0.8563 (m-30) cc_final: 0.8018 (t0) REVERT: E 259 LEU cc_start: 0.9365 (pt) cc_final: 0.9039 (tp) REVERT: E 305 VAL cc_start: 0.9385 (t) cc_final: 0.9157 (m) REVERT: E 436 LEU cc_start: 0.9214 (pp) cc_final: 0.8922 (mt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0985 time to fit residues: 31.7622 Evaluate side-chains 131 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 6.9990 chunk 168 optimal weight: 0.8980 chunk 129 optimal weight: 0.0050 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3407 r_free = 0.3407 target = 0.080429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.059873 restraints weight = 64239.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061671 restraints weight = 38784.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062587 restraints weight = 27397.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063423 restraints weight = 22642.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.063732 restraints weight = 19415.269| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4318 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= 0.159 Angle : 0.770 11.954 23775 Z= 0.368 Chirality : 0.047 0.356 2819 Planarity : 0.004 0.040 2872 Dihedral : 4.812 31.309 2222 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.51 (0.19), residues: 1975 helix: 0.88 (0.20), residues: 730 sheet: -1.58 (0.30), residues: 325 loop : -2.41 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 410 TYR 0.040 0.002 TYR A 262 PHE 0.040 0.002 PHE C 412 TRP 0.014 0.001 TRP C 168 HIS 0.008 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (17338) covalent geometry : angle 0.76072 / 0.37 (23675) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 0.95527 / 0.55 ( 10) hydrogen bonds : bond 0.04036 / 2.62 ( 648) hydrogen bonds : angle 4.37838 / 3.07 ( 1947) Misc. bond : bond 0.00327 / 0.17 ( 4) link_BETA1-3 : bond 0.00569 / 0.27 ( 2) link_BETA1-3 : angle 1.75231 / 1.13 ( 6) link_BETA1-4 : bond 0.00643 / 0.39 ( 14) link_BETA1-4 : angle 2.17534 / 1.31 ( 42) link_NAG-ASN : bond 0.00198 / 0.11 ( 14) link_NAG-ASN : angle 2.10681 / 1.70 ( 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 185 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9214 (m) cc_final: 0.8953 (p) REVERT: A 247 ASP cc_start: 0.8700 (m-30) cc_final: 0.8187 (t0) REVERT: A 254 PHE cc_start: 0.8876 (t80) cc_final: 0.8559 (t80) REVERT: A 302 ILE cc_start: 0.9793 (mt) cc_final: 0.9516 (tp) REVERT: B 210 MET cc_start: 0.8593 (tmm) cc_final: 0.8241 (tmm) REVERT: C 210 MET cc_start: 0.8589 (ppp) cc_final: 0.8382 (ppp) REVERT: C 221 LEU cc_start: 0.8350 (mm) cc_final: 0.7523 (tp) REVERT: C 254 PHE cc_start: 0.8841 (t80) cc_final: 0.8572 (t80) REVERT: C 417 ASP cc_start: 0.8367 (m-30) cc_final: 0.8106 (m-30) REVERT: D 302 ILE cc_start: 0.9697 (mp) cc_final: 0.9384 (tt) REVERT: D 331 TRP cc_start: 0.5601 (m100) cc_final: 0.4499 (m100) REVERT: E 247 ASP cc_start: 0.8665 (m-30) cc_final: 0.8073 (t0) REVERT: E 259 LEU cc_start: 0.9398 (pt) cc_final: 0.9082 (tp) REVERT: E 305 VAL cc_start: 0.9429 (t) cc_final: 0.9184 (m) REVERT: E 436 LEU cc_start: 0.9281 (pp) cc_final: 0.9002 (mt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0995 time to fit residues: 30.8401 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 : 0.665 ------------------------------------------------------------------------------- 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: 0.6980 chunk 117 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 HIS ** 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 = 0.3394 r_free = 0.3394 target = 0.079821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.059536 restraints weight = 63738.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.061113 restraints weight = 41142.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062147 restraints weight = 30554.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062534 restraints weight = 25113.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063013 restraints weight = 22754.520| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17377 Z= 0.164 Angle : 0.776 12.259 23775 Z= 0.368 Chirality : 0.048 0.357 2819 Planarity : 0.004 0.042 2872 Dihedral : 4.904 28.499 2222 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -1.48 (0.19), residues: 1975 helix: 0.89 (0.20), residues: 730 sheet: -1.55 (0.29), residues: 325 loop : -2.40 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.035 0.002 TYR A 262 PHE 0.027 0.002 PHE E 233 TRP 0.016 0.001 TRP C 94 HIS 0.008 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (17338) covalent geometry : angle 0.76652 / 0.37 (23675) SS BOND : bond 0.00106 / 0.05 ( 5) SS BOND : angle 0.94193 / 0.54 ( 10) hydrogen bonds : bond 0.04074 / 2.64 ( 648) hydrogen bonds : angle 4.37237 / 3.06 ( 1947) Misc. bond : bond 0.00323 / 0.17 ( 4) link_BETA1-3 : bond 0.00625 / 0.30 ( 2) link_BETA1-3 : angle 1.81512 / 1.18 ( 6) link_BETA1-4 : bond 0.00618 / 0.38 ( 14) link_BETA1-4 : angle 2.12744 / 1.29 ( 42) link_NAG-ASN : bond 0.00166 / 0.09 ( 14) link_NAG-ASN : angle 2.10779 / 1.72 ( 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 176 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9186 (m) cc_final: 0.8939 (p) REVERT: A 247 ASP cc_start: 0.8810 (m-30) cc_final: 0.8203 (t0) REVERT: A 302 ILE cc_start: 0.9788 (mt) cc_final: 0.9549 (tp) REVERT: B 210 MET cc_start: 0.8581 (tmm) cc_final: 0.8180 (tmm) REVERT: B 418 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8883 (mm-30) REVERT: C 221 LEU cc_start: 0.8382 (mm) cc_final: 0.7582 (tp) REVERT: C 254 PHE cc_start: 0.8814 (t80) cc_final: 0.8571 (t80) REVERT: C 417 ASP cc_start: 0.8350 (m-30) cc_final: 0.8091 (m-30) REVERT: C 436 LEU cc_start: 0.9181 (pp) cc_final: 0.8595 (mt) REVERT: D 302 ILE cc_start: 0.9707 (mp) cc_final: 0.9408 (tt) REVERT: D 331 TRP cc_start: 0.5662 (m100) cc_final: 0.4508 (m100) REVERT: E 247 ASP cc_start: 0.8628 (m-30) cc_final: 0.8046 (t0) REVERT: E 259 LEU cc_start: 0.9375 (pt) cc_final: 0.9028 (tp) REVERT: E 436 LEU cc_start: 0.9268 (pp) cc_final: 0.8981 (mt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0942 time to fit residues: 28.3745 Evaluate side-chains 115 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 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 132 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 130 optimal weight: 0.0370 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3422 r_free = 0.3422 target = 0.081529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.061502 restraints weight = 62847.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063180 restraints weight = 39890.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064007 restraints weight = 29226.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064768 restraints weight = 24572.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064999 restraints weight = 21458.071| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4562 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= 0.119 Angle : 0.780 13.675 23775 Z= 0.359 Chirality : 0.047 0.340 2819 Planarity : 0.004 0.041 2872 Dihedral : 4.770 26.751 2222 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1975 helix: 0.97 (0.20), residues: 730 sheet: -1.62 (0.28), residues: 355 loop : -2.28 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 410 TYR 0.038 0.001 TYR A 262 PHE 0.028 0.001 PHE C 412 TRP 0.012 0.001 TRP C 68 HIS 0.004 0.000 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (17338) covalent geometry : angle 0.77217 / 0.36 (23675) SS BOND : bond 0.00062 / 0.03 ( 5) SS BOND : angle 0.70524 / 0.41 ( 10) hydrogen bonds : bond 0.03972 / 2.57 ( 648) hydrogen bonds : angle 4.26089 / 2.98 ( 1947) Misc. bond : bond 0.00329 / 0.17 ( 4) link_BETA1-3 : bond 0.00670 / 0.32 ( 2) link_BETA1-3 : angle 1.74659 / 1.21 ( 6) link_BETA1-4 : bond 0.00646 / 0.40 ( 14) link_BETA1-4 : angle 2.13673 / 1.29 ( 42) link_NAG-ASN : bond 0.00191 / 0.11 ( 14) link_NAG-ASN : angle 1.89222 / 1.52 ( 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 178 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 THR cc_start: 0.9172 (m) cc_final: 0.8924 (p) REVERT: A 247 ASP cc_start: 0.8811 (m-30) cc_final: 0.8231 (t0) REVERT: A 254 PHE cc_start: 0.8825 (t80) cc_final: 0.8524 (t80) REVERT: A 258 LEU cc_start: 0.9634 (pt) cc_final: 0.9398 (pt) REVERT: A 296 ILE cc_start: 0.9384 (pt) cc_final: 0.9136 (tt) REVERT: A 302 ILE cc_start: 0.9777 (mt) cc_final: 0.9506 (tp) REVERT: B 42 ASP cc_start: 0.8173 (t70) cc_final: 0.7961 (t0) REVERT: B 210 MET cc_start: 0.8524 (tmm) cc_final: 0.8102 (tmm) REVERT: C 221 LEU cc_start: 0.8344 (mm) cc_final: 0.7513 (tp) REVERT: C 254 PHE cc_start: 0.8727 (t80) cc_final: 0.8484 (t80) REVERT: C 417 ASP cc_start: 0.8327 (m-30) cc_final: 0.8059 (m-30) REVERT: C 436 LEU cc_start: 0.9259 (pp) cc_final: 0.8698 (mt) REVERT: D 302 ILE cc_start: 0.9689 (mp) cc_final: 0.9398 (tt) REVERT: D 331 TRP cc_start: 0.5626 (m100) cc_final: 0.4470 (m100) REVERT: E 229 LEU cc_start: 0.9127 (pt) cc_final: 0.8762 (tt) REVERT: E 247 ASP cc_start: 0.8622 (m-30) cc_final: 0.8035 (t0) REVERT: E 259 LEU cc_start: 0.9354 (pt) cc_final: 0.9105 (tp) REVERT: E 305 VAL cc_start: 0.9420 (t) cc_final: 0.9173 (m) REVERT: E 436 LEU cc_start: 0.9236 (pp) cc_final: 0.8969 (mt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0941 time to fit residues: 28.7762 Evaluate side-chains 119 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 127 optimal weight: 0.5980 chunk 110 optimal weight: 0.4980 chunk 83 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3412 r_free = 0.3412 target = 0.080466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.060384 restraints weight = 63208.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.061998 restraints weight = 40399.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062830 restraints weight = 29965.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.063526 restraints weight = 25059.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063726 restraints weight = 22051.904| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4657 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= 0.123 Angle : 0.767 13.455 23775 Z= 0.354 Chirality : 0.047 0.346 2819 Planarity : 0.004 0.041 2872 Dihedral : 4.706 24.672 2222 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -1.56 (0.28), residues: 355 loop : -2.25 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 410 TYR 0.037 0.001 TYR A 262 PHE 0.025 0.001 PHE E 233 TRP 0.011 0.001 TRP C 68 HIS 0.002 0.000 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17338) covalent geometry : angle 0.75885 / 0.35 (23675) SS BOND : bond 0.00071 / 0.04 ( 5) SS BOND : angle 0.75981 / 0.43 ( 10) hydrogen bonds : bond 0.03919 / 2.54 ( 648) hydrogen bonds : angle 4.25063 / 2.98 ( 1947) Misc. bond : bond 0.00314 / 0.16 ( 4) link_BETA1-3 : bond 0.00560 / 0.27 ( 2) link_BETA1-3 : angle 1.68964 / 1.13 ( 6) link_BETA1-4 : bond 0.00646 / 0.40 ( 14) link_BETA1-4 : angle 2.11696 / 1.28 ( 42) link_NAG-ASN : bond 0.00185 / 0.10 ( 14) link_NAG-ASN : angle 1.92857 / 1.56 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.63 seconds wall clock time: 42 minutes 33.47 seconds (2553.47 seconds total)