Starting phenix.real_space_refine on Sat Sep 12 06:07:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pm0_20382/09_2026/6pm0_20382.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9165 2.51 5 N 2250 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 14080 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 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: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.44, per 1000 atoms: 0.17 Number of scatterers: 14080 At special positions: 0 Unit cell: (104.521, 105.344, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2565 8.00 N 2250 7.00 C 9165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 25 sheets defined 41.0% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.819A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.203A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.610A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.986A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.651A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 4.161A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 427 removed outlier: 3.962A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.525A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 removed outlier: 3.819A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.203A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.611A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.986A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 266 through 285 removed outlier: 3.652A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 4.161A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 427 removed outlier: 3.962A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.526A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.819A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.204A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.611A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.986A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 266 through 285 removed outlier: 3.652A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 4.162A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 427 removed outlier: 3.962A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.526A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 32 removed outlier: 3.820A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.203A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.611A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.986A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.652A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 4.162A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 427 removed outlier: 3.962A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 405 " --> pdb=" O ARG D 401 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.525A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 32 removed outlier: 3.820A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.203A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.610A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.986A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 266 through 285 removed outlier: 3.651A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 4.161A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 427 removed outlier: 3.962A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.526A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 417 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.449A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.418A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.449A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.418A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.449A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.418A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.449A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.418A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.449A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.418A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 720 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2221 1.32 - 1.46: 4953 1.46 - 1.59: 7086 1.59 - 1.73: 5 1.73 - 1.87: 160 Bond restraints: 14425 Sorted by residual: bond pdb=" C MET B 34 " pdb=" O MET B 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.59e+01 bond pdb=" C MET D 34 " pdb=" O MET D 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET A 34 " pdb=" O MET A 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET E 34 " pdb=" O MET E 34 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.43e-02 4.89e+03 1.58e+01 bond pdb=" C MET C 34 " pdb=" O MET C 34 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.43e-02 4.89e+03 1.54e+01 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 19359 3.45 - 6.90: 207 6.90 - 10.35: 16 10.35 - 13.80: 13 13.80 - 17.24: 5 Bond angle restraints: 19600 Sorted by residual: angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" CB MET E 34 " pdb=" CG MET E 34 " pdb=" SD MET E 34 " ideal model delta sigma weight residual 112.70 95.46 17.24 3.00e+00 1.11e-01 3.30e+01 ... (remaining 19595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 7991 15.20 - 30.41: 404 30.41 - 45.61: 75 45.61 - 60.82: 10 60.82 - 76.02: 5 Dihedral angle restraints: 8485 sinusoidal: 3370 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN E 160 " pdb=" C ASN E 160 " pdb=" N PHE E 161 " pdb=" CA PHE E 161 " ideal model delta harmonic sigma weight residual 180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual 180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1687 0.059 - 0.117: 470 0.117 - 0.176: 88 0.176 - 0.235: 10 0.235 - 0.294: 5 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2257 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 128 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C THR E 128 " -0.037 2.00e-02 2.50e+03 pdb=" O THR E 128 " 0.014 2.00e-02 2.50e+03 pdb=" N THR E 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C THR B 128 " 0.037 2.00e-02 2.50e+03 pdb=" O THR B 128 " -0.014 2.00e-02 2.50e+03 pdb=" N THR B 129 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 128 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C THR C 128 " -0.037 2.00e-02 2.50e+03 pdb=" O THR C 128 " 0.014 2.00e-02 2.50e+03 pdb=" N THR C 129 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4339 2.82 - 3.34: 12176 3.34 - 3.86: 23038 3.86 - 4.38: 27074 4.38 - 4.90: 45280 Nonbonded interactions: 111907 Sorted by model distance: nonbonded pdb=" OG SER D 27 " pdb=" NE ARG E 43 " model vdw 2.298 3.120 nonbonded pdb=" O THR E 281 " pdb=" OG SER E 284 " model vdw 2.333 3.040 nonbonded pdb=" O THR D 281 " pdb=" OG SER D 284 " model vdw 2.334 3.040 nonbonded pdb=" O THR A 281 " pdb=" OG SER A 284 " model vdw 2.334 3.040 nonbonded pdb=" O THR C 281 " pdb=" OG SER C 284 " model vdw 2.334 3.040 ... (remaining 111902 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 0.072 14450 Z= 0.330 Angle : 1.045 17.244 19665 Z= 0.530 Chirality : 0.057 0.294 2260 Planarity : 0.007 0.049 2425 Dihedral : 9.717 76.020 5135 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -4.55 (0.15), residues: 1710 helix: -4.56 (0.10), residues: 565 sheet: -0.97 (0.26), residues: 350 loop : -2.71 (0.16), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 147 TYR 0.025 0.003 TYR E 144 PHE 0.024 0.003 PHE C 115 TRP 0.019 0.003 TRP B 110 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.33 (14425) covalent geometry : angle 1.03382 / 0.53 (19600) SS BOND : bond 0.00423 / 0.24 ( 10) SS BOND : angle 3.88706 / 2.86 ( 20) hydrogen bonds : bond 0.28563 / 18.43 ( 575) hydrogen bonds : angle 9.51149 / 6.58 ( 2070) link_BETA1-4 : bond 0.00282 / 0.17 ( 10) link_BETA1-4 : angle 1.80212 / 1.16 ( 30) link_NAG-ASN : bond 0.00279 / 0.16 ( 5) link_NAG-ASN : angle 2.68280 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 VAL cc_start: 0.6445 (t) cc_final: 0.5698 (t) REVERT: E 320 VAL cc_start: 0.6564 (t) cc_final: 0.5838 (t) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.1135 time to fit residues: 63.7125 Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 82 GLN B 62 ASN B 82 GLN B 131 ASN C 62 ASN C 82 GLN C 131 ASN D 62 ASN D 82 GLN D 131 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 82 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074730 restraints weight = 30061.282| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.02 r_work: 0.2897 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14450 Z= 0.149 Angle : 0.671 7.468 19665 Z= 0.348 Chirality : 0.044 0.179 2260 Planarity : 0.004 0.029 2425 Dihedral : 6.058 40.668 1880 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 10.93 % Favored : 87.35 % 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: -3.33 (0.17), residues: 1710 helix: -2.82 (0.15), residues: 595 sheet: -0.57 (0.26), residues: 345 loop : -2.40 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 287 TYR 0.015 0.001 TYR B 317 PHE 0.015 0.001 PHE A 414 TRP 0.012 0.002 TRP E 255 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14425) covalent geometry : angle 0.66460 / 0.35 (19600) SS BOND : bond 0.00575 / 0.34 ( 10) SS BOND : angle 2.38088 / 1.50 ( 20) hydrogen bonds : bond 0.05655 / 3.66 ( 575) hydrogen bonds : angle 5.56275 / 3.83 ( 2070) link_BETA1-4 : bond 0.00464 / 0.30 ( 10) link_BETA1-4 : angle 1.56398 / 1.00 ( 30) link_NAG-ASN : bond 0.00109 / 0.06 ( 5) link_NAG-ASN : angle 1.23132 / 0.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.8549 (p0) cc_final: 0.8277 (m-30) REVERT: A 314 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 28 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8614 (tm-30) REVERT: B 242 GLN cc_start: 0.8144 (tt0) cc_final: 0.7658 (tp40) REVERT: B 243 MET cc_start: 0.8882 (mmm) cc_final: 0.8667 (mmm) REVERT: C 242 GLN cc_start: 0.8264 (tt0) cc_final: 0.7876 (tp40) REVERT: D 268 ARG cc_start: 0.6706 (mtp85) cc_final: 0.6501 (mtp180) REVERT: D 320 VAL cc_start: 0.5101 (t) cc_final: 0.4598 (t) REVERT: E 28 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 242 GLN cc_start: 0.8155 (tt0) cc_final: 0.7843 (tp40) outliers start: 26 outliers final: 11 residues processed: 241 average time/residue: 0.0915 time to fit residues: 34.3086 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 58 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074863 restraints weight = 30129.509| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.01 r_work: 0.2884 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14450 Z= 0.130 Angle : 0.587 6.340 19665 Z= 0.308 Chirality : 0.043 0.194 2260 Planarity : 0.003 0.023 2425 Dihedral : 5.484 36.560 1880 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.12 % Allowed : 12.19 % Favored : 85.70 % 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: -2.36 (0.18), residues: 1710 helix: -1.54 (0.19), residues: 595 sheet: -0.30 (0.27), residues: 345 loop : -2.13 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 229 TYR 0.015 0.001 TYR D 317 PHE 0.010 0.001 PHE B 322 TRP 0.011 0.001 TRP C 302 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14425) covalent geometry : angle 0.58303 / 0.31 (19600) SS BOND : bond 0.01447 / 0.92 ( 10) SS BOND : angle 1.41777 / 1.02 ( 20) hydrogen bonds : bond 0.04717 / 3.07 ( 575) hydrogen bonds : angle 4.73875 / 3.26 ( 2070) link_BETA1-4 : bond 0.00424 / 0.25 ( 10) link_BETA1-4 : angle 1.41336 / 0.95 ( 30) link_NAG-ASN : bond 0.00011 / 0.01 ( 5) link_NAG-ASN : angle 0.93940 / 0.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8990 (mtm) cc_final: 0.8543 (mmm) REVERT: A 282 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8716 (mm-40) REVERT: A 300 ASP cc_start: 0.8480 (p0) cc_final: 0.8226 (m-30) REVERT: A 314 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 214 CYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6516 (p) REVERT: B 242 GLN cc_start: 0.8111 (tt0) cc_final: 0.7844 (tp40) REVERT: B 243 MET cc_start: 0.8987 (mmm) cc_final: 0.8733 (mmm) REVERT: C 242 GLN cc_start: 0.8031 (tt0) cc_final: 0.7720 (tp40) REVERT: D 282 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8697 (mm-40) REVERT: D 314 LEU cc_start: 0.8945 (mt) cc_final: 0.8227 (tt) REVERT: D 320 VAL cc_start: 0.5204 (t) cc_final: 0.4700 (t) REVERT: E 28 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8634 (tm-30) REVERT: E 314 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7837 (tt) outliers start: 32 outliers final: 19 residues processed: 226 average time/residue: 0.0984 time to fit residues: 34.3489 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 0.0170 chunk 106 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 231 HIS ** E 235 GLN ** 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 = 0.3618 r_free = 0.3618 target = 0.104289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073994 restraints weight = 29733.873| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.01 r_work: 0.2868 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14450 Z= 0.139 Angle : 0.588 7.426 19665 Z= 0.301 Chirality : 0.044 0.201 2260 Planarity : 0.003 0.044 2425 Dihedral : 5.182 32.293 1880 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.25 % Allowed : 12.98 % Favored : 83.77 % 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: -1.63 (0.19), residues: 1710 helix: -0.61 (0.20), residues: 595 sheet: -0.01 (0.28), residues: 345 loop : -1.96 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.014 0.001 TYR C 317 PHE 0.010 0.001 PHE B 115 TRP 0.036 0.002 TRP D 255 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14425) covalent geometry : angle 0.58355 / 0.30 (19600) SS BOND : bond 0.00400 / 0.24 ( 10) SS BOND : angle 1.46923 / 1.05 ( 20) hydrogen bonds : bond 0.04095 / 2.67 ( 575) hydrogen bonds : angle 4.44637 / 3.07 ( 2070) link_BETA1-4 : bond 0.00378 / 0.23 ( 10) link_BETA1-4 : angle 1.41766 / 0.96 ( 30) link_NAG-ASN : bond 0.00047 / 0.03 ( 5) link_NAG-ASN : angle 0.89514 / 0.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8999 (mtm) cc_final: 0.8767 (mmm) REVERT: A 156 MET cc_start: 0.9154 (mmm) cc_final: 0.8826 (mmt) REVERT: A 300 ASP cc_start: 0.8537 (p0) cc_final: 0.8167 (m-30) REVERT: A 314 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7867 (tt) REVERT: A 317 TYR cc_start: 0.8707 (t80) cc_final: 0.8482 (t80) REVERT: B 28 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (tm-30) REVERT: E 28 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8521 (tm-30) REVERT: E 242 GLN cc_start: 0.8364 (tp40) cc_final: 0.7918 (tp40) REVERT: E 314 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.7894 (tt) outliers start: 49 outliers final: 35 residues processed: 212 average time/residue: 0.0888 time to fit residues: 29.7424 Evaluate side-chains 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 141 ASN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 141 ASN C 82 GLN C 141 ASN D 82 GLN D 141 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 141 ASN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070964 restraints weight = 30015.493| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.98 r_work: 0.2795 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14450 Z= 0.240 Angle : 0.650 8.196 19665 Z= 0.332 Chirality : 0.045 0.189 2260 Planarity : 0.004 0.025 2425 Dihedral : 5.358 29.399 1880 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.44 % Allowed : 14.44 % Favored : 82.12 % 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: -1.02 (0.19), residues: 1710 helix: 0.08 (0.21), residues: 590 sheet: 0.19 (0.28), residues: 345 loop : -1.68 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 43 TYR 0.014 0.002 TYR B 144 PHE 0.015 0.002 PHE A 115 TRP 0.018 0.002 TRP C 255 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (14425) covalent geometry : angle 0.64335 / 0.33 (19600) SS BOND : bond 0.00685 / 0.38 ( 10) SS BOND : angle 2.07179 / 1.32 ( 20) hydrogen bonds : bond 0.04242 / 2.78 ( 575) hydrogen bonds : angle 4.50527 / 3.10 ( 2070) link_BETA1-4 : bond 0.00331 / 0.21 ( 10) link_BETA1-4 : angle 1.55242 / 1.08 ( 30) link_NAG-ASN : bond 0.00316 / 0.18 ( 5) link_NAG-ASN : angle 1.30559 / 0.72 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8995 (mtm) cc_final: 0.8699 (mmm) REVERT: A 156 MET cc_start: 0.9136 (mmm) cc_final: 0.8904 (mmt) REVERT: A 243 MET cc_start: 0.9002 (mmm) cc_final: 0.8693 (mmm) REVERT: A 300 ASP cc_start: 0.8523 (p0) cc_final: 0.8182 (m-30) REVERT: A 314 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 207 GLU cc_start: 0.8855 (tt0) cc_final: 0.8571 (tm-30) REVERT: C 207 GLU cc_start: 0.9050 (tt0) cc_final: 0.8642 (tm-30) REVERT: C 242 GLN cc_start: 0.8231 (tp40) cc_final: 0.7789 (tp40) REVERT: D 241 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8887 (mp) REVERT: E 242 GLN cc_start: 0.8329 (tp40) cc_final: 0.7874 (mm110) REVERT: E 271 LEU cc_start: 0.7963 (mt) cc_final: 0.7727 (mt) REVERT: E 317 TYR cc_start: 0.8751 (t80) cc_final: 0.8456 (t80) outliers start: 52 outliers final: 34 residues processed: 226 average time/residue: 0.0888 time to fit residues: 31.9432 Evaluate side-chains 217 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN D 235 GLN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072840 restraints weight = 29628.384| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.98 r_work: 0.2832 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14450 Z= 0.143 Angle : 0.606 12.061 19665 Z= 0.308 Chirality : 0.044 0.202 2260 Planarity : 0.003 0.034 2425 Dihedral : 5.200 38.991 1880 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.78 % Allowed : 15.30 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1710 helix: 0.42 (0.22), residues: 600 sheet: 0.34 (0.29), residues: 345 loop : -1.67 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 287 TYR 0.012 0.001 TYR C 317 PHE 0.011 0.001 PHE A 115 TRP 0.009 0.001 TRP B 255 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14425) covalent geometry : angle 0.60009 / 0.31 (19600) SS BOND : bond 0.00572 / 0.33 ( 10) SS BOND : angle 2.25611 / 1.21 ( 20) hydrogen bonds : bond 0.03885 / 2.56 ( 575) hydrogen bonds : angle 4.15483 / 2.85 ( 2070) link_BETA1-4 : bond 0.00366 / 0.22 ( 10) link_BETA1-4 : angle 1.33316 / 0.92 ( 30) link_NAG-ASN : bond 0.00071 / 0.04 ( 5) link_NAG-ASN : angle 0.95397 / 0.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8105 (tmm) REVERT: A 72 MET cc_start: 0.8959 (mtm) cc_final: 0.8659 (mmm) REVERT: A 207 GLU cc_start: 0.8912 (tt0) cc_final: 0.8594 (tm-30) REVERT: A 300 ASP cc_start: 0.8522 (p0) cc_final: 0.8022 (m-30) REVERT: A 314 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7884 (tt) REVERT: B 130 ASP cc_start: 0.8893 (m-30) cc_final: 0.8611 (m-30) REVERT: B 156 MET cc_start: 0.9263 (mmt) cc_final: 0.8906 (mmt) REVERT: B 207 GLU cc_start: 0.8802 (tt0) cc_final: 0.8579 (tm-30) REVERT: C 207 GLU cc_start: 0.8970 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 242 GLN cc_start: 0.8251 (tp40) cc_final: 0.7816 (tp40) REVERT: E 242 GLN cc_start: 0.8331 (tp40) cc_final: 0.7952 (tp40) REVERT: E 271 LEU cc_start: 0.7987 (mt) cc_final: 0.7753 (mt) REVERT: E 314 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7901 (tt) outliers start: 42 outliers final: 26 residues processed: 219 average time/residue: 0.0959 time to fit residues: 32.5521 Evaluate side-chains 215 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 0.9980 chunk 132 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 115 optimal weight: 0.0000 chunk 154 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 202 GLN C 82 GLN C 202 GLN D 82 GLN E 82 GLN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075299 restraints weight = 29474.801| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.99 r_work: 0.2890 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14450 Z= 0.104 Angle : 0.570 8.016 19665 Z= 0.288 Chirality : 0.043 0.197 2260 Planarity : 0.003 0.022 2425 Dihedral : 4.918 46.720 1880 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.85 % Allowed : 15.70 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1710 helix: 0.80 (0.22), residues: 595 sheet: 0.48 (0.29), residues: 345 loop : -1.63 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.012 0.001 TYR C 317 PHE 0.008 0.001 PHE B 115 TRP 0.048 0.002 TRP A 255 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14425) covalent geometry : angle 0.56473 / 0.29 (19600) SS BOND : bond 0.00364 / 0.22 ( 10) SS BOND : angle 1.94900 / 1.02 ( 20) hydrogen bonds : bond 0.03551 / 2.32 ( 575) hydrogen bonds : angle 3.86270 / 2.66 ( 2070) link_BETA1-4 : bond 0.00379 / 0.23 ( 10) link_BETA1-4 : angle 1.25523 / 0.84 ( 30) link_NAG-ASN : bond 0.00040 / 0.03 ( 5) link_NAG-ASN : angle 0.68493 / 0.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8130 (tmm) REVERT: A 72 MET cc_start: 0.8949 (mtm) cc_final: 0.8655 (mmm) REVERT: A 207 GLU cc_start: 0.8880 (tt0) cc_final: 0.8596 (tm-30) REVERT: A 236 MET cc_start: 0.8403 (mmm) cc_final: 0.8161 (mmm) REVERT: A 300 ASP cc_start: 0.8467 (p0) cc_final: 0.7912 (m-30) REVERT: B 130 ASP cc_start: 0.8817 (m-30) cc_final: 0.8543 (m-30) REVERT: C 207 GLU cc_start: 0.8960 (tt0) cc_final: 0.8694 (tm-30) REVERT: C 212 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8328 (ptp90) REVERT: C 242 GLN cc_start: 0.8287 (tp40) cc_final: 0.8024 (tp40) REVERT: D 207 GLU cc_start: 0.8881 (tt0) cc_final: 0.8628 (tm-30) REVERT: E 72 MET cc_start: 0.8994 (mtm) cc_final: 0.8522 (mmm) REVERT: E 242 GLN cc_start: 0.8350 (tp40) cc_final: 0.8004 (tp40) outliers start: 28 outliers final: 12 residues processed: 216 average time/residue: 0.0938 time to fit residues: 32.1061 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 137 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 0.0470 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 193 GLN C 82 GLN D 82 GLN E 82 GLN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073252 restraints weight = 29517.101| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.96 r_work: 0.2838 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14450 Z= 0.174 Angle : 0.611 8.328 19665 Z= 0.310 Chirality : 0.044 0.178 2260 Planarity : 0.003 0.024 2425 Dihedral : 4.984 45.337 1880 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.52 % Allowed : 16.36 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1710 helix: 0.93 (0.23), residues: 600 sheet: 0.49 (0.28), residues: 345 loop : -1.54 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.011 0.001 TYR A 317 PHE 0.013 0.001 PHE B 115 TRP 0.062 0.002 TRP A 255 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (14425) covalent geometry : angle 0.60352 / 0.31 (19600) SS BOND : bond 0.00472 / 0.28 ( 10) SS BOND : angle 2.44124 / 1.35 ( 20) hydrogen bonds : bond 0.03647 / 2.38 ( 575) hydrogen bonds : angle 4.00222 / 2.74 ( 2070) link_BETA1-4 : bond 0.00351 / 0.21 ( 10) link_BETA1-4 : angle 1.38998 / 0.95 ( 30) link_NAG-ASN : bond 0.00185 / 0.11 ( 5) link_NAG-ASN : angle 1.07582 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: A 72 MET cc_start: 0.8973 (mtm) cc_final: 0.8684 (mmm) REVERT: A 207 GLU cc_start: 0.8939 (tt0) cc_final: 0.8630 (tm-30) REVERT: A 300 ASP cc_start: 0.8503 (p0) cc_final: 0.7986 (m-30) REVERT: B 130 ASP cc_start: 0.8836 (m-30) cc_final: 0.8556 (m-30) REVERT: C 207 GLU cc_start: 0.9056 (tt0) cc_final: 0.8717 (tm-30) REVERT: C 212 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8330 (ptp90) REVERT: C 242 GLN cc_start: 0.8285 (tp40) cc_final: 0.7806 (tp40) REVERT: C 317 TYR cc_start: 0.8653 (t80) cc_final: 0.8438 (t80) REVERT: D 242 GLN cc_start: 0.8386 (tp40) cc_final: 0.7813 (tp40) REVERT: E 242 GLN cc_start: 0.8341 (tp40) cc_final: 0.8012 (tp40) outliers start: 23 outliers final: 14 residues processed: 200 average time/residue: 0.0963 time to fit residues: 30.2273 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 138 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN B 231 HIS E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072958 restraints weight = 29682.565| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.00 r_work: 0.2840 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14450 Z= 0.167 Angle : 0.596 7.873 19665 Z= 0.304 Chirality : 0.044 0.170 2260 Planarity : 0.003 0.020 2425 Dihedral : 5.045 46.044 1880 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.46 % Allowed : 16.42 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1710 helix: 1.06 (0.23), residues: 600 sheet: 0.74 (0.30), residues: 320 loop : -1.29 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.011 0.001 TYR A 317 PHE 0.013 0.001 PHE B 115 TRP 0.050 0.002 TRP A 255 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14425) covalent geometry : angle 0.58930 / 0.30 (19600) SS BOND : bond 0.00439 / 0.27 ( 10) SS BOND : angle 2.34922 / 1.30 ( 20) hydrogen bonds : bond 0.03607 / 2.36 ( 575) hydrogen bonds : angle 3.98685 / 2.73 ( 2070) link_BETA1-4 : bond 0.00343 / 0.21 ( 10) link_BETA1-4 : angle 1.34007 / 0.92 ( 30) link_NAG-ASN : bond 0.00144 / 0.08 ( 5) link_NAG-ASN : angle 1.06971 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: A 72 MET cc_start: 0.8979 (mtm) cc_final: 0.8679 (mmm) REVERT: A 207 GLU cc_start: 0.8870 (tt0) cc_final: 0.8602 (tm-30) REVERT: A 300 ASP cc_start: 0.8511 (p0) cc_final: 0.7937 (m-30) REVERT: B 130 ASP cc_start: 0.8854 (m-30) cc_final: 0.8587 (m-30) REVERT: C 207 GLU cc_start: 0.8965 (tt0) cc_final: 0.8664 (tm-30) REVERT: C 212 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8358 (ptp90) REVERT: C 317 TYR cc_start: 0.8656 (t80) cc_final: 0.8433 (t80) REVERT: C 423 ILE cc_start: 0.8847 (tt) cc_final: 0.8601 (mm) REVERT: D 72 MET cc_start: 0.9114 (mmm) cc_final: 0.8697 (mmm) REVERT: D 207 GLU cc_start: 0.8892 (tt0) cc_final: 0.8635 (tm-30) REVERT: D 241 ILE cc_start: 0.9326 (mt) cc_final: 0.9109 (mp) REVERT: D 242 GLN cc_start: 0.8373 (tp40) cc_final: 0.7751 (tp40) REVERT: E 72 MET cc_start: 0.9012 (mtm) cc_final: 0.8658 (mmm) REVERT: E 242 GLN cc_start: 0.8367 (tp40) cc_final: 0.8037 (tp40) REVERT: E 314 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.7992 (tt) outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.0939 time to fit residues: 30.8149 Evaluate side-chains 203 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 125 optimal weight: 0.0370 chunk 139 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 166 optimal weight: 0.0870 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 GLN ** E 235 GLN ** 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 = 0.3638 r_free = 0.3638 target = 0.105982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075568 restraints weight = 29467.280| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.01 r_work: 0.2885 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14450 Z= 0.103 Angle : 0.583 8.033 19665 Z= 0.293 Chirality : 0.043 0.172 2260 Planarity : 0.003 0.022 2425 Dihedral : 4.837 45.262 1880 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.13 % Allowed : 17.09 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1710 helix: 1.14 (0.23), residues: 595 sheet: 0.80 (0.30), residues: 320 loop : -1.29 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.010 0.001 TYR A 317 PHE 0.009 0.001 PHE B 115 TRP 0.042 0.002 TRP A 255 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (14425) covalent geometry : angle 0.57643 / 0.29 (19600) SS BOND : bond 0.00480 / 0.27 ( 10) SS BOND : angle 2.45153 / 1.34 ( 20) hydrogen bonds : bond 0.03331 / 2.18 ( 575) hydrogen bonds : angle 3.80206 / 2.61 ( 2070) link_BETA1-4 : bond 0.00354 / 0.20 ( 10) link_BETA1-4 : angle 1.21897 / 0.82 ( 30) link_NAG-ASN : bond 0.00073 / 0.04 ( 5) link_NAG-ASN : angle 0.64688 / 0.35 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (tmm) REVERT: A 72 MET cc_start: 0.8960 (mtm) cc_final: 0.8678 (mmm) REVERT: A 156 MET cc_start: 0.9226 (mmm) cc_final: 0.8882 (mmt) REVERT: A 207 GLU cc_start: 0.8856 (tt0) cc_final: 0.8608 (tm-30) REVERT: A 300 ASP cc_start: 0.8530 (p0) cc_final: 0.7947 (m-30) REVERT: A 314 LEU cc_start: 0.8800 (mt) cc_final: 0.7942 (tt) REVERT: B 130 ASP cc_start: 0.8839 (m-30) cc_final: 0.8589 (m-30) REVERT: B 179 MET cc_start: 0.9152 (tpt) cc_final: 0.8933 (mmt) REVERT: C 207 GLU cc_start: 0.8952 (tt0) cc_final: 0.8683 (tm-30) REVERT: C 212 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (ptp90) REVERT: C 242 GLN cc_start: 0.8233 (tp40) cc_final: 0.7815 (tp40) REVERT: D 72 MET cc_start: 0.9082 (mmm) cc_final: 0.8679 (mmm) REVERT: D 207 GLU cc_start: 0.8933 (tt0) cc_final: 0.8709 (tm-30) REVERT: D 242 GLN cc_start: 0.8408 (tp40) cc_final: 0.7985 (tp40) REVERT: E 72 MET cc_start: 0.8985 (mtm) cc_final: 0.8647 (mmm) REVERT: E 242 GLN cc_start: 0.8376 (tp40) cc_final: 0.8048 (tp40) outliers start: 17 outliers final: 12 residues processed: 208 average time/residue: 0.1024 time to fit residues: 33.8835 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 125 optimal weight: 0.1980 chunk 165 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN E 193 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073204 restraints weight = 29661.951| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.99 r_work: 0.2840 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14450 Z= 0.164 Angle : 0.605 7.990 19665 Z= 0.306 Chirality : 0.044 0.166 2260 Planarity : 0.003 0.023 2425 Dihedral : 4.913 45.244 1880 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.26 % Allowed : 17.42 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1710 helix: 1.28 (0.23), residues: 595 sheet: 0.79 (0.30), residues: 320 loop : -1.22 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 212 TYR 0.010 0.001 TYR A 144 PHE 0.022 0.001 PHE B 322 TRP 0.045 0.002 TRP E 255 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (14425) covalent geometry : angle 0.59711 / 0.30 (19600) SS BOND : bond 0.00449 / 0.28 ( 10) SS BOND : angle 2.63720 / 1.47 ( 20) hydrogen bonds : bond 0.03418 / 2.24 ( 575) hydrogen bonds : angle 3.92727 / 2.70 ( 2070) link_BETA1-4 : bond 0.00363 / 0.23 ( 10) link_BETA1-4 : angle 1.40294 / 0.96 ( 30) link_NAG-ASN : bond 0.00220 / 0.13 ( 5) link_NAG-ASN : angle 1.07737 / 0.59 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.24 seconds wall clock time: 56 minutes 0.50 seconds (3360.50 seconds total)