Starting phenix.real_space_refine on Wed Mar 4 14:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pm0_20382/03_2026/6pm0_20382.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pm0_20382/03_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_20382/03_2026/6pm0_20382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pm0_20382/03_2026/6pm0_20382.map" model { file = "/net/cci-nas-00/data/ceres_data/6pm0_20382/03_2026/6pm0_20382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pm0_20382/03_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-dev-5986/lib/python3.9/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 dihedrals: 9 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: 2.35, 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: 0.93 Conformation dependent library (CDL) restraints added in 612.1 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: 0.53 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: 2.19 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 - 20.76: 8470 20.76 - 41.51: 250 41.51 - 62.27: 15 62.27 - 83.02: 35 83.02 - 103.78: 20 Dihedral angle restraints: 8790 sinusoidal: 3675 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 8787 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: 0.04 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.870 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 12.784 103.778 5440 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 covalent geometry : bond 0.00739 (14425) covalent geometry : angle 1.03382 (19600) SS BOND : bond 0.00423 ( 10) SS BOND : angle 3.88706 ( 20) hydrogen bonds : bond 0.28563 ( 575) hydrogen bonds : angle 9.51149 ( 2070) link_BETA1-4 : bond 0.00282 ( 10) link_BETA1-4 : angle 1.80212 ( 30) link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.68280 ( 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 : 0.488 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: 0.1178 time to fit residues: 65.3945 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 E 131 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074743 restraints weight = 29736.864| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.13 r_work: 0.2891 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14450 Z= 0.152 Angle : 0.694 7.468 19665 Z= 0.355 Chirality : 0.045 0.163 2260 Planarity : 0.004 0.030 2425 Dihedral : 10.112 63.991 2185 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.66 % Allowed : 10.79 % Favored : 87.55 % 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: -3.30 (0.17), residues: 1710 helix: -2.81 (0.15), residues: 590 sheet: -0.56 (0.26), residues: 345 loop : -2.39 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 268 TYR 0.018 0.002 TYR B 317 PHE 0.018 0.001 PHE A 414 TRP 0.014 0.002 TRP A 302 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00320 (14425) covalent geometry : angle 0.68301 (19600) SS BOND : bond 0.00505 ( 10) SS BOND : angle 2.38203 ( 20) hydrogen bonds : bond 0.05439 ( 575) hydrogen bonds : angle 5.50433 ( 2070) link_BETA1-4 : bond 0.00454 ( 10) link_BETA1-4 : angle 2.44588 ( 30) link_NAG-ASN : bond 0.00036 ( 5) link_NAG-ASN : angle 1.27622 ( 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 262 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.8615 (p0) cc_final: 0.8353 (m-30) REVERT: A 314 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 28 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: B 242 GLN cc_start: 0.8173 (tt0) cc_final: 0.7694 (tp40) REVERT: B 243 MET cc_start: 0.8866 (mmm) cc_final: 0.8653 (mmm) REVERT: C 28 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 242 GLN cc_start: 0.8292 (tt0) cc_final: 0.7854 (tp40) REVERT: C 243 MET cc_start: 0.9027 (mmm) cc_final: 0.8722 (mmm) REVERT: C 300 ASP cc_start: 0.8544 (p0) cc_final: 0.8321 (m-30) REVERT: E 28 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8577 (tm-30) REVERT: E 242 GLN cc_start: 0.8189 (tt0) cc_final: 0.7876 (tp40) outliers start: 25 outliers final: 11 residues processed: 245 average time/residue: 0.1002 time to fit residues: 38.1587 Evaluate side-chains 203 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3628 r_free = 0.3628 target = 0.105786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074764 restraints weight = 29929.249| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.10 r_work: 0.2897 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14450 Z= 0.126 Angle : 0.606 6.414 19665 Z= 0.312 Chirality : 0.044 0.188 2260 Planarity : 0.003 0.028 2425 Dihedral : 6.872 35.595 2185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.25 % Allowed : 12.32 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.18), residues: 1710 helix: -1.46 (0.19), residues: 595 sheet: -0.10 (0.27), residues: 340 loop : -2.12 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.014 0.001 TYR D 317 PHE 0.010 0.001 PHE D 115 TRP 0.029 0.002 TRP B 255 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00274 (14425) covalent geometry : angle 0.59741 (19600) SS BOND : bond 0.00424 ( 10) SS BOND : angle 1.76954 ( 20) hydrogen bonds : bond 0.04559 ( 575) hydrogen bonds : angle 4.63557 ( 2070) link_BETA1-4 : bond 0.00541 ( 10) link_BETA1-4 : angle 2.24897 ( 30) link_NAG-ASN : bond 0.00026 ( 5) link_NAG-ASN : angle 0.95406 ( 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 253 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8958 (mtm) cc_final: 0.8716 (mmm) REVERT: A 242 GLN cc_start: 0.8146 (tt0) cc_final: 0.7580 (tp40) REVERT: A 243 MET cc_start: 0.9024 (mmm) cc_final: 0.8787 (mmm) REVERT: A 300 ASP cc_start: 0.8536 (p0) cc_final: 0.8295 (m-30) REVERT: A 314 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.7949 (tt) REVERT: B 28 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8574 (tm-30) REVERT: B 242 GLN cc_start: 0.8156 (tt0) cc_final: 0.7885 (tp40) REVERT: B 243 MET cc_start: 0.8986 (mmm) cc_final: 0.8736 (mmm) REVERT: B 320 VAL cc_start: 0.5101 (t) cc_final: 0.4884 (t) REVERT: D 173 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7886 (mm-30) REVERT: D 314 LEU cc_start: 0.8958 (mt) cc_final: 0.8235 (tt) REVERT: E 28 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8659 (tm-30) REVERT: E 314 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.7853 (tt) outliers start: 34 outliers final: 20 residues processed: 225 average time/residue: 0.0951 time to fit residues: 33.4179 Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 303 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 170 MET Chi-restraints excluded: chain B residue 253 LEU 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 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 303 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 170 MET 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: 0.8980 chunk 129 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 106 optimal weight: 0.0040 chunk 119 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3621 r_free = 0.3621 target = 0.105540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.074120 restraints weight = 29676.528| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.16 r_work: 0.2879 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14450 Z= 0.133 Angle : 0.588 7.573 19665 Z= 0.298 Chirality : 0.044 0.195 2260 Planarity : 0.003 0.040 2425 Dihedral : 5.483 30.323 2185 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.91 % Allowed : 13.05 % Favored : 84.04 % 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: -1.52 (0.19), residues: 1710 helix: -0.48 (0.21), residues: 595 sheet: 0.10 (0.28), residues: 345 loop : -1.95 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.016 0.001 TYR C 317 PHE 0.010 0.001 PHE B 115 TRP 0.034 0.002 TRP D 255 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00295 (14425) covalent geometry : angle 0.57997 (19600) SS BOND : bond 0.00550 ( 10) SS BOND : angle 1.77228 ( 20) hydrogen bonds : bond 0.03959 ( 575) hydrogen bonds : angle 4.34737 ( 2070) link_BETA1-4 : bond 0.00428 ( 10) link_BETA1-4 : angle 2.11308 ( 30) link_NAG-ASN : bond 0.00059 ( 5) link_NAG-ASN : angle 0.89477 ( 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 249 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8974 (mtm) cc_final: 0.8652 (mmm) REVERT: A 242 GLN cc_start: 0.8113 (tt0) cc_final: 0.7639 (tp40) REVERT: A 243 MET cc_start: 0.9040 (mmm) cc_final: 0.8782 (mmm) REVERT: A 300 ASP cc_start: 0.8554 (p0) cc_final: 0.8137 (m-30) REVERT: A 314 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 317 TYR cc_start: 0.8652 (t80) cc_final: 0.8421 (t80) REVERT: B 28 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: B 179 MET cc_start: 0.9207 (tpt) cc_final: 0.8797 (tpt) REVERT: B 243 MET cc_start: 0.8992 (mmm) cc_final: 0.8732 (mmm) REVERT: B 314 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.7983 (tt) REVERT: D 173 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7945 (mm-30) REVERT: E 242 GLN cc_start: 0.8323 (tp40) cc_final: 0.8040 (tp40) REVERT: E 314 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 44 outliers final: 32 residues processed: 219 average time/residue: 0.0937 time to fit residues: 32.4772 Evaluate side-chains 219 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 303 MET 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 170 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 LEU 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 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 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 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: 0.9980 chunk 121 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 58 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS C 141 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3620 r_free = 0.3620 target = 0.105540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074067 restraints weight = 29826.829| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.16 r_work: 0.2868 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3574 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= 0.132 Angle : 0.577 8.288 19665 Z= 0.292 Chirality : 0.044 0.197 2260 Planarity : 0.003 0.021 2425 Dihedral : 5.281 24.206 2185 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.25 % Allowed : 14.64 % 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: -0.99 (0.19), residues: 1710 helix: 0.24 (0.21), residues: 595 sheet: 0.27 (0.28), residues: 345 loop : -1.83 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.016 0.001 TYR D 317 PHE 0.010 0.001 PHE A 115 TRP 0.014 0.001 TRP D 255 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00295 (14425) covalent geometry : angle 0.56942 (19600) SS BOND : bond 0.00411 ( 10) SS BOND : angle 2.03638 ( 20) hydrogen bonds : bond 0.03762 ( 575) hydrogen bonds : angle 4.12851 ( 2070) link_BETA1-4 : bond 0.00412 ( 10) link_BETA1-4 : angle 1.83265 ( 30) link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.88565 ( 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 252 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8971 (mtm) cc_final: 0.8619 (mmm) REVERT: A 242 GLN cc_start: 0.8122 (tt0) cc_final: 0.7672 (tp40) REVERT: A 243 MET cc_start: 0.9046 (mmm) cc_final: 0.8768 (mmm) REVERT: A 300 ASP cc_start: 0.8581 (p0) cc_final: 0.8025 (m-30) REVERT: A 314 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.7901 (tt) REVERT: B 179 MET cc_start: 0.9215 (tpt) cc_final: 0.8757 (tpt) REVERT: B 207 GLU cc_start: 0.8759 (tt0) cc_final: 0.8544 (tm-30) REVERT: B 314 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.7921 (tt) REVERT: C 173 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8088 (tt0) REVERT: D 173 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7915 (mm-30) REVERT: E 72 MET cc_start: 0.9089 (mmm) cc_final: 0.8855 (mmm) REVERT: E 242 GLN cc_start: 0.8334 (tp40) cc_final: 0.8056 (tp40) REVERT: E 314 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7927 (tt) REVERT: E 317 TYR cc_start: 0.8675 (t80) cc_final: 0.8418 (t80) outliers start: 49 outliers final: 27 residues processed: 220 average time/residue: 0.0939 time to fit residues: 32.8079 Evaluate side-chains 214 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 303 MET 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 170 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 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 202 GLN Chi-restraints excluded: chain C residue 214 CYS 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 129 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 202 GLN 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 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: 4.9990 chunk 25 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 141 ASN A 235 GLN B 82 GLN B 141 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN 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 = 0.3578 r_free = 0.3578 target = 0.103257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.071459 restraints weight = 29719.496| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.15 r_work: 0.2805 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14450 Z= 0.215 Angle : 0.627 7.880 19665 Z= 0.319 Chirality : 0.045 0.172 2260 Planarity : 0.003 0.033 2425 Dihedral : 5.442 22.283 2185 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.05 % Allowed : 15.23 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1710 helix: 0.58 (0.22), residues: 600 sheet: 0.35 (0.28), residues: 345 loop : -1.61 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 287 TYR 0.014 0.002 TYR C 317 PHE 0.013 0.001 PHE A 115 TRP 0.039 0.002 TRP A 255 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00491 (14425) covalent geometry : angle 0.61751 (19600) SS BOND : bond 0.00467 ( 10) SS BOND : angle 2.52208 ( 20) hydrogen bonds : bond 0.03922 ( 575) hydrogen bonds : angle 4.18361 ( 2070) link_BETA1-4 : bond 0.00285 ( 10) link_BETA1-4 : angle 1.84123 ( 30) link_NAG-ASN : bond 0.00324 ( 5) link_NAG-ASN : angle 1.29535 ( 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 236 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8080 (tmm) REVERT: A 72 MET cc_start: 0.8983 (mtm) cc_final: 0.8641 (mmm) REVERT: A 120 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8932 (ttmm) REVERT: A 300 ASP cc_start: 0.8612 (p0) cc_final: 0.8090 (m-30) REVERT: A 314 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.7858 (tt) REVERT: B 207 GLU cc_start: 0.8830 (tt0) cc_final: 0.8572 (tm-30) REVERT: B 243 MET cc_start: 0.9016 (mmm) cc_final: 0.8708 (mmm) REVERT: B 314 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 207 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: E 72 MET cc_start: 0.9089 (mmm) cc_final: 0.8832 (mmm) REVERT: E 105 MET cc_start: 0.8983 (mmm) cc_final: 0.8776 (mmm) REVERT: E 173 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8213 (tt0) REVERT: E 242 GLN cc_start: 0.8374 (tp40) cc_final: 0.7948 (tp40) REVERT: E 314 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.7939 (tt) outliers start: 46 outliers final: 32 residues processed: 212 average time/residue: 0.0910 time to fit residues: 30.5922 Evaluate side-chains 220 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 120 LYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 303 MET 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 170 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 314 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 202 GLN Chi-restraints excluded: chain C residue 207 GLU 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 253 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 202 GLN 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: 0.0170 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 115 optimal weight: 0.0050 chunk 154 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 82 GLN D 82 GLN D 235 GLN E 82 GLN E 131 ASN 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 = 0.3620 r_free = 0.3620 target = 0.105906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074294 restraints weight = 29492.843| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.18 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14450 Z= 0.106 Angle : 0.588 13.315 19665 Z= 0.295 Chirality : 0.043 0.188 2260 Planarity : 0.003 0.023 2425 Dihedral : 5.212 38.059 2185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.25 % Allowed : 15.70 % Favored : 82.05 % 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: -0.42 (0.20), residues: 1710 helix: 0.87 (0.22), residues: 595 sheet: 0.47 (0.29), residues: 345 loop : -1.58 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 287 TYR 0.010 0.001 TYR A 317 PHE 0.009 0.001 PHE B 115 TRP 0.022 0.001 TRP A 255 HIS 0.003 0.001 HIS C 217 Details of bonding type rmsd covalent geometry : bond 0.00231 (14425) covalent geometry : angle 0.57920 (19600) SS BOND : bond 0.00604 ( 10) SS BOND : angle 2.59578 ( 20) hydrogen bonds : bond 0.03573 ( 575) hydrogen bonds : angle 3.90841 ( 2070) link_BETA1-4 : bond 0.00398 ( 10) link_BETA1-4 : angle 1.62647 ( 30) link_NAG-ASN : bond 0.00012 ( 5) link_NAG-ASN : angle 0.82309 ( 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 233 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8057 (tmm) REVERT: A 72 MET cc_start: 0.8974 (mtm) cc_final: 0.8649 (mmm) REVERT: A 207 GLU cc_start: 0.8898 (tt0) cc_final: 0.8582 (tm-30) REVERT: A 242 GLN cc_start: 0.7994 (tt0) cc_final: 0.7605 (tp40) REVERT: A 243 MET cc_start: 0.9027 (mmm) cc_final: 0.8794 (mmm) REVERT: A 300 ASP cc_start: 0.8611 (p0) cc_final: 0.7896 (m-30) REVERT: B 207 GLU cc_start: 0.8817 (tt0) cc_final: 0.8601 (tm-30) REVERT: B 243 MET cc_start: 0.8972 (mmm) cc_final: 0.8697 (mmm) REVERT: C 212 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (ptp90) REVERT: D 72 MET cc_start: 0.9122 (mmm) cc_final: 0.8680 (mmm) REVERT: E 72 MET cc_start: 0.9081 (mmm) cc_final: 0.8821 (mmm) REVERT: E 105 MET cc_start: 0.8981 (mmm) cc_final: 0.8758 (mmm) REVERT: E 207 GLU cc_start: 0.8907 (tt0) cc_final: 0.8630 (tm-30) REVERT: E 242 GLN cc_start: 0.8361 (tp40) cc_final: 0.7975 (tp40) outliers start: 34 outliers final: 14 residues processed: 205 average time/residue: 0.0926 time to fit residues: 29.9671 Evaluate side-chains 197 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 310 VAL 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: 3.9990 chunk 60 optimal weight: 0.0030 chunk 137 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073271 restraints weight = 29473.747| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.14 r_work: 0.2845 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14450 Z= 0.142 Angle : 0.580 8.768 19665 Z= 0.294 Chirality : 0.043 0.161 2260 Planarity : 0.003 0.020 2425 Dihedral : 5.185 46.076 2185 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.52 % Allowed : 16.42 % Favored : 82.05 % 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: -0.31 (0.20), residues: 1710 helix: 1.00 (0.23), residues: 600 sheet: 0.49 (0.28), residues: 345 loop : -1.55 (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 0.012 0.001 PHE E 115 TRP 0.018 0.001 TRP A 255 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00326 (14425) covalent geometry : angle 0.57073 (19600) SS BOND : bond 0.00424 ( 10) SS BOND : angle 2.60026 ( 20) hydrogen bonds : bond 0.03531 ( 575) hydrogen bonds : angle 3.89388 ( 2070) link_BETA1-4 : bond 0.00357 ( 10) link_BETA1-4 : angle 1.67963 ( 30) link_NAG-ASN : bond 0.00205 ( 5) link_NAG-ASN : angle 1.03049 ( 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 206 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8094 (tmm) REVERT: A 72 MET cc_start: 0.8986 (mtm) cc_final: 0.8677 (mmm) REVERT: A 156 MET cc_start: 0.9232 (mmm) cc_final: 0.8918 (mmt) REVERT: A 207 GLU cc_start: 0.8937 (tt0) cc_final: 0.8607 (tm-30) REVERT: A 242 GLN cc_start: 0.7945 (tt0) cc_final: 0.7615 (tp40) REVERT: A 243 MET cc_start: 0.9048 (mmm) cc_final: 0.8808 (mmm) REVERT: A 300 ASP cc_start: 0.8613 (p0) cc_final: 0.7934 (m-30) REVERT: B 207 GLU cc_start: 0.8825 (tt0) cc_final: 0.8593 (tm-30) REVERT: B 243 MET cc_start: 0.8966 (mmm) cc_final: 0.8701 (mmm) REVERT: C 212 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8361 (ptt-90) REVERT: C 241 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8755 (mp) REVERT: D 241 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9049 (mp) REVERT: D 242 GLN cc_start: 0.8394 (tp40) cc_final: 0.7786 (tp40) REVERT: E 72 MET cc_start: 0.9098 (mmm) cc_final: 0.8858 (mmm) REVERT: E 105 MET cc_start: 0.8992 (mmm) cc_final: 0.8772 (mmm) REVERT: E 242 GLN cc_start: 0.8365 (tp40) cc_final: 0.8034 (tp40) REVERT: E 317 TYR cc_start: 0.8646 (t80) cc_final: 0.8423 (t80) outliers start: 23 outliers final: 15 residues processed: 194 average time/residue: 0.0929 time to fit residues: 28.5647 Evaluate side-chains 198 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 A residue 202 GLN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 MET 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 212 ARG Chi-restraints excluded: chain C residue 241 ILE 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 E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 214 CYS 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: 9.9990 chunk 138 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 0.2980 chunk 115 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.104616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.072770 restraints weight = 29645.083| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.17 r_work: 0.2833 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14450 Z= 0.147 Angle : 0.590 8.559 19665 Z= 0.298 Chirality : 0.043 0.166 2260 Planarity : 0.003 0.021 2425 Dihedral : 5.184 45.300 2185 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.46 % Allowed : 16.69 % Favored : 81.85 % 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: -0.08 (0.20), residues: 1710 helix: 1.08 (0.23), residues: 600 sheet: 0.78 (0.30), residues: 320 loop : -1.33 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.010 0.001 TYR A 317 PHE 0.013 0.001 PHE E 115 TRP 0.016 0.001 TRP A 255 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00338 (14425) covalent geometry : angle 0.57977 (19600) SS BOND : bond 0.00415 ( 10) SS BOND : angle 2.76402 ( 20) hydrogen bonds : bond 0.03490 ( 575) hydrogen bonds : angle 3.88890 ( 2070) link_BETA1-4 : bond 0.00368 ( 10) link_BETA1-4 : angle 1.62154 ( 30) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 1.05828 ( 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 209 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8155 (tmm) REVERT: A 72 MET cc_start: 0.8983 (mtm) cc_final: 0.8684 (mmm) REVERT: A 156 MET cc_start: 0.9239 (mmm) cc_final: 0.8915 (mmt) REVERT: A 207 GLU cc_start: 0.8927 (tt0) cc_final: 0.8622 (tm-30) REVERT: A 242 GLN cc_start: 0.7958 (tt0) cc_final: 0.7636 (tp40) REVERT: A 243 MET cc_start: 0.9035 (mmm) cc_final: 0.8784 (mmm) REVERT: A 300 ASP cc_start: 0.8630 (p0) cc_final: 0.7916 (m-30) REVERT: B 243 MET cc_start: 0.8954 (mmm) cc_final: 0.8668 (mmm) REVERT: C 212 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8401 (ptp90) REVERT: C 241 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8740 (mp) REVERT: D 242 GLN cc_start: 0.8395 (tp40) cc_final: 0.7817 (tp40) REVERT: E 72 MET cc_start: 0.9119 (mmm) cc_final: 0.8881 (mmm) REVERT: E 105 MET cc_start: 0.8981 (mmm) cc_final: 0.8768 (mmm) REVERT: E 207 GLU cc_start: 0.8928 (tt0) cc_final: 0.8639 (tm-30) REVERT: E 242 GLN cc_start: 0.8333 (tp40) cc_final: 0.8049 (tp40) REVERT: E 317 TYR cc_start: 0.8646 (t80) cc_final: 0.8409 (t80) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 0.0938 time to fit residues: 28.9566 Evaluate side-chains 197 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 A residue 202 GLN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 MET 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 212 ARG Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 170 MET 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 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 166 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3617 r_free = 0.3617 target = 0.105634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073925 restraints weight = 29609.864| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.16 r_work: 0.2861 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14450 Z= 0.116 Angle : 0.581 7.982 19665 Z= 0.292 Chirality : 0.043 0.168 2260 Planarity : 0.003 0.035 2425 Dihedral : 5.076 45.733 2185 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.32 % Allowed : 17.09 % Favored : 81.59 % 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: 0.01 (0.20), residues: 1710 helix: 1.17 (0.23), residues: 600 sheet: 0.83 (0.30), residues: 320 loop : -1.30 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 287 TYR 0.010 0.001 TYR A 317 PHE 0.010 0.001 PHE B 115 TRP 0.014 0.001 TRP A 255 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00262 (14425) covalent geometry : angle 0.57226 (19600) SS BOND : bond 0.00372 ( 10) SS BOND : angle 2.55240 ( 20) hydrogen bonds : bond 0.03351 ( 575) hydrogen bonds : angle 3.79211 ( 2070) link_BETA1-4 : bond 0.00384 ( 10) link_BETA1-4 : angle 1.55446 ( 30) link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.90564 ( 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 211 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8163 (tmm) REVERT: A 72 MET cc_start: 0.8964 (mtm) cc_final: 0.8620 (mmm) REVERT: A 207 GLU cc_start: 0.8917 (tt0) cc_final: 0.8616 (tm-30) REVERT: A 242 GLN cc_start: 0.7929 (tt0) cc_final: 0.7644 (tp40) REVERT: A 243 MET cc_start: 0.9022 (mmm) cc_final: 0.8763 (mmm) REVERT: A 300 ASP cc_start: 0.8621 (p0) cc_final: 0.7877 (m-30) REVERT: A 303 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7393 (ttt) REVERT: A 314 LEU cc_start: 0.8797 (mt) cc_final: 0.7923 (tt) REVERT: B 156 MET cc_start: 0.9226 (mmt) cc_final: 0.8948 (mmt) REVERT: B 243 MET cc_start: 0.8938 (mmm) cc_final: 0.8679 (mmm) REVERT: B 423 ILE cc_start: 0.8844 (tt) cc_final: 0.8594 (mm) REVERT: C 241 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8997 (mp) REVERT: C 242 GLN cc_start: 0.8256 (tp40) cc_final: 0.7975 (tp40) REVERT: D 72 MET cc_start: 0.9123 (mmm) cc_final: 0.8837 (mmm) REVERT: D 207 GLU cc_start: 0.8976 (tt0) cc_final: 0.8678 (tm-30) REVERT: D 242 GLN cc_start: 0.8445 (tp40) cc_final: 0.7951 (tp40) REVERT: E 72 MET cc_start: 0.9095 (mmm) cc_final: 0.8854 (mmm) REVERT: E 105 MET cc_start: 0.8989 (mmm) cc_final: 0.8770 (mmm) REVERT: E 207 GLU cc_start: 0.8929 (tt0) cc_final: 0.8650 (tm-30) REVERT: E 242 GLN cc_start: 0.8334 (tp40) cc_final: 0.8064 (tp40) outliers start: 20 outliers final: 13 residues processed: 200 average time/residue: 0.0915 time to fit residues: 29.0845 Evaluate side-chains 199 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 A residue 202 GLN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 MET 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 241 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.104803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073073 restraints weight = 29604.768| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.15 r_work: 0.2840 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4183 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= 0.141 Angle : 0.584 8.083 19665 Z= 0.294 Chirality : 0.043 0.165 2260 Planarity : 0.003 0.021 2425 Dihedral : 5.083 45.226 2185 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.52 % Allowed : 17.35 % Favored : 81.13 % 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: 1.27 (0.23), residues: 600 sheet: 0.84 (0.30), residues: 320 loop : -1.25 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 212 TYR 0.010 0.001 TYR A 317 PHE 0.012 0.001 PHE B 115 TRP 0.014 0.001 TRP A 255 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00324 (14425) covalent geometry : angle 0.57481 (19600) SS BOND : bond 0.00410 ( 10) SS BOND : angle 2.57862 ( 20) hydrogen bonds : bond 0.03357 ( 575) hydrogen bonds : angle 3.81508 ( 2070) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 1.60337 ( 30) link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 1.05757 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3254.69 seconds wall clock time: 56 minutes 28.42 seconds (3388.42 seconds total)