Starting phenix.real_space_refine on Thu Sep 26 22:43:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plq_20372/09_2024/6plq_20372.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 9270 2.51 5 N 2290 2.21 5 O 2580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14240 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" 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: {'ABU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F, I, H, J Time building chain proxies: 6.68, per 1000 atoms: 0.47 Number of scatterers: 14240 At special positions: 0 Unit cell: (105.786, 107.745, 135.824, 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 2580 8.00 N 2290 7.00 C 9270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.19 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 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: 3.66 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 60 helices and 25 sheets defined 39.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.233A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.234A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 245 through 256 removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.234A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 30 through 35 Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.998A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 106 removed outlier: 4.039A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 425 removed outlier: 4.053A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.233A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.999A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.040A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 245 through 256 removed outlier: 4.462A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 264 through 285 removed outlier: 3.755A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 325 removed outlier: 3.575A pdb=" N MET E 303 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 425 removed outlier: 4.052A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.233A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU A 99 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.415A 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 123 removed outlier: 3.721A pdb=" N ASN A 123 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 228 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 227 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 212 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS A 216 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 223 " --> pdb=" O LYS A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.415A 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 123 removed outlier: 3.721A pdb=" N ASN B 123 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.794A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 228 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 227 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 212 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS B 216 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 223 " --> pdb=" O LYS B 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.565A pdb=" N LEU C 99 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.415A 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 123 removed outlier: 3.721A pdb=" N ASN C 123 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 228 " --> pdb=" O MET C 170 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 227 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 212 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS C 216 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 223 " --> pdb=" O LYS C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU D 99 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.416A 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 123 removed outlier: 3.721A pdb=" N ASN D 123 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.794A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 228 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 227 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 212 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.789A pdb=" N LYS D 216 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 223 " --> pdb=" O LYS D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 3.566A pdb=" N LEU E 99 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.415A 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 123 removed outlier: 3.721A pdb=" N ASN E 123 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.691A 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 removed outlier: 3.795A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 228 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 227 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 212 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 165 through 167 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 removed outlier: 3.790A pdb=" N LYS E 216 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 223 " --> pdb=" O LYS E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 565 hydrogen bonds defined for protein. 1635 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: 4.33 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4385 1.34 - 1.46: 3523 1.46 - 1.58: 6507 1.58 - 1.70: 0 1.70 - 1.81: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 19286 1.34 - 2.67: 354 2.67 - 4.01: 75 4.01 - 5.35: 45 5.35 - 6.69: 15 Bond angle restraints: 19775 Sorted by residual: angle pdb=" CB ABU C 504 " pdb=" CG ABU C 504 " pdb=" CD ABU C 504 " ideal model delta sigma weight residual 116.08 109.39 6.69 3.00e+00 1.11e-01 4.97e+00 angle pdb=" CB ABU B 504 " pdb=" CG ABU B 504 " pdb=" CD ABU B 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.96e+00 angle pdb=" CB ABU A 504 " pdb=" CG ABU A 504 " pdb=" CD ABU A 504 " ideal model delta sigma weight residual 116.08 109.40 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" CB ABU D 504 " pdb=" CG ABU D 504 " pdb=" CD ABU D 504 " ideal model delta sigma weight residual 116.08 109.43 6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CB ABU E 504 " pdb=" CG ABU E 504 " pdb=" CD ABU E 504 " ideal model delta sigma weight residual 116.08 109.44 6.64 3.00e+00 1.11e-01 4.90e+00 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8705 21.75 - 43.50: 150 43.50 - 65.24: 1 65.24 - 86.99: 30 86.99 - 108.74: 20 Dihedral angle restraints: 8906 sinusoidal: 3791 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 36.41 56.59 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" O4 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C5 BMA J 3 " pdb=" O5 BMA J 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.97 108.74 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.97 108.74 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 8903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2059 0.078 - 0.156: 196 0.156 - 0.235: 0 0.235 - 0.313: 5 0.313 - 0.391: 5 Chirality restraints: 2265 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.82e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.80e+02 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 103 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO C 411 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " 0.016 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 108 2.60 - 3.18: 11514 3.18 - 3.75: 20733 3.75 - 4.33: 29951 4.33 - 4.90: 48490 Nonbonded interactions: 110796 Sorted by model distance: nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " model vdw 2.193 3.760 ... (remaining 110791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.360 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 31.580 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14585 Z= 0.131 Angle : 0.526 6.685 19775 Z= 0.258 Chirality : 0.046 0.391 2265 Planarity : 0.003 0.028 2450 Dihedral : 11.125 108.738 5580 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.15), residues: 1710 helix: -4.20 (0.11), residues: 465 sheet: -2.53 (0.24), residues: 335 loop : -2.31 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 422 HIS 0.001 0.000 HIS C 125 PHE 0.003 0.001 PHE B 258 TYR 0.004 0.000 TYR D 74 ARG 0.002 0.000 ARG E 234 *********************** 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 409 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3253 time to fit residues: 183.0467 Evaluate side-chains 240 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 44 optimal weight: 0.0270 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN B 62 ASN B 125 HIS B 131 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 77 ASN C 125 HIS ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 131 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN E 62 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS E 131 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4331 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14585 Z= 0.214 Angle : 0.773 8.639 19775 Z= 0.378 Chirality : 0.049 0.168 2265 Planarity : 0.005 0.043 2450 Dihedral : 9.549 62.334 2200 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.32 % Allowed : 13.55 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.17), residues: 1710 helix: -2.40 (0.19), residues: 500 sheet: -1.90 (0.25), residues: 335 loop : -2.09 (0.18), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 186 HIS 0.018 0.004 HIS E 125 PHE 0.034 0.002 PHE E 79 TYR 0.018 0.001 TYR C 144 ARG 0.007 0.001 ARG A 147 *********************** 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 301 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 265 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.2604 (OUTLIER) cc_final: 0.2339 (mm) REVERT: A 119 GLU cc_start: 0.2687 (OUTLIER) cc_final: 0.2465 (tt0) REVERT: A 163 MET cc_start: 0.6420 (mmm) cc_final: 0.6028 (mmm) REVERT: B 106 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2720 (mm) REVERT: B 163 MET cc_start: 0.6317 (mmm) cc_final: 0.6003 (mmm) REVERT: B 171 GLN cc_start: 0.7455 (pt0) cc_final: 0.7043 (pm20) REVERT: C 106 LEU cc_start: 0.3039 (OUTLIER) cc_final: 0.2761 (mm) REVERT: C 133 LEU cc_start: 0.5196 (tp) cc_final: 0.4461 (tt) REVERT: C 163 MET cc_start: 0.6396 (mmm) cc_final: 0.5920 (mmm) REVERT: C 171 GLN cc_start: 0.7353 (pt0) cc_final: 0.6924 (pm20) REVERT: D 106 LEU cc_start: 0.2990 (OUTLIER) cc_final: 0.2706 (mm) REVERT: D 163 MET cc_start: 0.6336 (mmm) cc_final: 0.5931 (mmm) REVERT: D 171 GLN cc_start: 0.7339 (pt0) cc_final: 0.7063 (pm20) REVERT: D 262 MET cc_start: 0.1004 (tpt) cc_final: 0.0752 (tpt) REVERT: E 106 LEU cc_start: 0.2829 (OUTLIER) cc_final: 0.2527 (mm) REVERT: E 171 GLN cc_start: 0.7433 (pt0) cc_final: 0.7121 (pm20) REVERT: E 214 CYS cc_start: 0.3987 (OUTLIER) cc_final: 0.2819 (p) outliers start: 36 outliers final: 14 residues processed: 288 average time/residue: 0.2520 time to fit residues: 106.4853 Evaluate side-chains 198 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 236 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 0.2980 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4625 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14585 Z= 0.219 Angle : 0.767 8.314 19775 Z= 0.374 Chirality : 0.047 0.190 2265 Planarity : 0.004 0.028 2450 Dihedral : 7.303 50.250 2200 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.77 % Allowed : 14.52 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.18), residues: 1710 helix: -1.35 (0.21), residues: 525 sheet: -1.38 (0.23), residues: 425 loop : -2.05 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 84 HIS 0.004 0.002 HIS D 217 PHE 0.025 0.002 PHE A 414 TYR 0.023 0.002 TYR A 317 ARG 0.007 0.001 ARG A 268 *********************** 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 259 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.0275 (OUTLIER) cc_final: -0.0688 (mt) REVERT: B 101 LEU cc_start: 0.1295 (OUTLIER) cc_final: 0.0674 (mt) REVERT: B 133 LEU cc_start: 0.5695 (tp) cc_final: 0.4942 (tt) REVERT: B 171 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: C 171 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: D 171 GLN cc_start: 0.7400 (pt0) cc_final: 0.7005 (pm20) REVERT: D 214 CYS cc_start: 0.4551 (OUTLIER) cc_final: 0.3836 (p) REVERT: E 101 LEU cc_start: 0.0588 (OUTLIER) cc_final: -0.0439 (mt) REVERT: E 163 MET cc_start: 0.6454 (mmm) cc_final: 0.6205 (mmm) REVERT: E 171 GLN cc_start: 0.7508 (pt0) cc_final: 0.7034 (pm20) REVERT: E 214 CYS cc_start: 0.4573 (OUTLIER) cc_final: 0.3881 (p) outliers start: 43 outliers final: 20 residues processed: 253 average time/residue: 0.2580 time to fit residues: 98.5500 Evaluate side-chains 215 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 TRP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 214 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 0.0050 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 131 ASN A 141 ASN A 171 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 171 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4918 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14585 Z= 0.200 Angle : 0.750 12.316 19775 Z= 0.357 Chirality : 0.046 0.188 2265 Planarity : 0.004 0.031 2450 Dihedral : 5.953 52.432 2200 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.84 % Allowed : 16.00 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.19), residues: 1710 helix: -0.74 (0.23), residues: 520 sheet: -1.00 (0.27), residues: 345 loop : -2.03 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.003 0.001 HIS B 217 PHE 0.020 0.002 PHE B 414 TYR 0.020 0.002 TYR D 317 ARG 0.006 0.001 ARG C 268 *********************** 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 260 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.558 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 156 MET cc_start: 0.6631 (mmt) cc_final: 0.6157 (mmm) REVERT: A 410 PHE cc_start: 0.6963 (m-10) cc_final: 0.6642 (m-80) REVERT: B 133 LEU cc_start: 0.6248 (tp) cc_final: 0.5794 (tt) REVERT: B 163 MET cc_start: 0.6689 (mmm) cc_final: 0.6457 (mmm) REVERT: C 141 ASN cc_start: 0.6762 (m-40) cc_final: 0.6240 (m-40) REVERT: C 163 MET cc_start: 0.6711 (mmm) cc_final: 0.6465 (mmm) REVERT: C 410 PHE cc_start: 0.6774 (m-10) cc_final: 0.6544 (m-10) REVERT: D 171 GLN cc_start: 0.7660 (pt0) cc_final: 0.6875 (pm20) REVERT: D 410 PHE cc_start: 0.6891 (m-10) cc_final: 0.6555 (m-80) REVERT: E 60 PHE cc_start: 0.4583 (t80) cc_final: 0.4019 (t80) REVERT: E 131 ASN cc_start: 0.4633 (p0) cc_final: 0.3795 (p0) REVERT: E 171 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: E 410 PHE cc_start: 0.6897 (m-10) cc_final: 0.6691 (m-10) outliers start: 44 outliers final: 33 residues processed: 253 average time/residue: 0.2238 time to fit residues: 87.0996 Evaluate side-chains 226 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 84 TRP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.0370 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 418 ASN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 1.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 14585 Z= 0.449 Angle : 1.063 17.744 19775 Z= 0.541 Chirality : 0.057 0.346 2265 Planarity : 0.007 0.123 2450 Dihedral : 6.874 55.175 2200 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 4.32 % Allowed : 17.10 % Favored : 78.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1710 helix: -0.77 (0.23), residues: 520 sheet: -1.18 (0.29), residues: 325 loop : -1.54 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 84 HIS 0.015 0.005 HIS C 125 PHE 0.037 0.003 PHE B 29 TYR 0.027 0.003 TYR B 175 ARG 0.018 0.002 ARG C 147 *********************** 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 335 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 268 time to evaluate : 1.470 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 151 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7234 (m) REVERT: A 156 MET cc_start: 0.8086 (mmt) cc_final: 0.7743 (mmp) REVERT: A 171 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: B 82 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8044 (tm-30) REVERT: B 156 MET cc_start: 0.7233 (mmt) cc_final: 0.6999 (mmt) REVERT: B 171 GLN cc_start: 0.8000 (pt0) cc_final: 0.7070 (pm20) REVERT: B 202 GLN cc_start: 0.7802 (pm20) cc_final: 0.7297 (mp-120) REVERT: C 171 GLN cc_start: 0.8089 (pt0) cc_final: 0.6972 (pm20) REVERT: D 24 MET cc_start: 0.2512 (ttt) cc_final: 0.2250 (ttt) REVERT: D 171 GLN cc_start: 0.8340 (pt0) cc_final: 0.7070 (pm20) REVERT: D 202 GLN cc_start: 0.7899 (pm20) cc_final: 0.7552 (mp10) REVERT: E 82 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 142 VAL cc_start: 0.8225 (t) cc_final: 0.7603 (m) REVERT: E 171 GLN cc_start: 0.8236 (pt0) cc_final: 0.7066 (pm20) outliers start: 67 outliers final: 44 residues processed: 323 average time/residue: 0.1961 time to fit residues: 99.7070 Evaluate side-chains 280 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 406 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 1.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14585 Z= 0.192 Angle : 0.827 15.964 19775 Z= 0.385 Chirality : 0.047 0.247 2265 Planarity : 0.004 0.053 2450 Dihedral : 5.935 50.493 2200 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.16 % Allowed : 21.35 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1710 helix: -0.60 (0.23), residues: 540 sheet: -0.44 (0.29), residues: 365 loop : -1.50 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 84 HIS 0.004 0.002 HIS D 125 PHE 0.019 0.002 PHE E 115 TYR 0.017 0.001 TYR B 218 ARG 0.011 0.001 ARG A 268 *********************** 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 289 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8210 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 202 GLN cc_start: 0.7872 (pm20) cc_final: 0.7156 (pm20) REVERT: A 415 LEU cc_start: 0.8545 (pp) cc_final: 0.8210 (tt) REVERT: B 156 MET cc_start: 0.6943 (mmt) cc_final: 0.6743 (mmt) REVERT: B 202 GLN cc_start: 0.7724 (pm20) cc_final: 0.7161 (mp-120) REVERT: B 415 LEU cc_start: 0.8563 (pp) cc_final: 0.8336 (tt) REVERT: C 82 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7980 (tt0) REVERT: C 415 LEU cc_start: 0.8452 (pp) cc_final: 0.8088 (tt) REVERT: D 24 MET cc_start: 0.2872 (ttt) cc_final: 0.2390 (ttt) REVERT: D 168 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7203 (p) REVERT: D 262 MET cc_start: 0.0918 (tpt) cc_final: 0.0657 (mmm) REVERT: D 415 LEU cc_start: 0.8529 (pp) cc_final: 0.8220 (tt) REVERT: E 24 MET cc_start: 0.2518 (ttt) cc_final: 0.2207 (ttt) REVERT: E 82 GLN cc_start: 0.8267 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 168 CYS cc_start: 0.7149 (p) cc_final: 0.6672 (p) REVERT: E 202 GLN cc_start: 0.8123 (pm20) cc_final: 0.7323 (pm20) REVERT: E 415 LEU cc_start: 0.8545 (pp) cc_final: 0.8227 (tt) outliers start: 49 outliers final: 33 residues processed: 282 average time/residue: 0.2043 time to fit residues: 90.9732 Evaluate side-chains 264 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 406 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 1.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14585 Z= 0.201 Angle : 0.824 12.177 19775 Z= 0.381 Chirality : 0.047 0.309 2265 Planarity : 0.004 0.031 2450 Dihedral : 5.613 51.970 2200 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.39 % Allowed : 22.71 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1710 helix: -0.16 (0.24), residues: 515 sheet: -0.79 (0.29), residues: 340 loop : -1.18 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 84 HIS 0.010 0.002 HIS A 217 PHE 0.024 0.002 PHE A 60 TYR 0.022 0.001 TYR A 317 ARG 0.007 0.000 ARG C 75 *********************** 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 282 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 156 MET cc_start: 0.7910 (mmt) cc_final: 0.7522 (mmm) REVERT: A 202 GLN cc_start: 0.8000 (pm20) cc_final: 0.7316 (pm20) REVERT: A 242 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 415 LEU cc_start: 0.8599 (pp) cc_final: 0.8383 (tt) REVERT: B 82 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8104 (tt0) REVERT: B 156 MET cc_start: 0.7020 (mmt) cc_final: 0.6803 (mmm) REVERT: B 202 GLN cc_start: 0.7794 (pm20) cc_final: 0.7442 (pm20) REVERT: B 242 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6834 (tm-30) REVERT: C 168 CYS cc_start: 0.7430 (p) cc_final: 0.6939 (p) REVERT: C 202 GLN cc_start: 0.8287 (pm20) cc_final: 0.7916 (pm20) REVERT: C 415 LEU cc_start: 0.8571 (pp) cc_final: 0.8350 (tt) REVERT: D 24 MET cc_start: 0.3439 (ttt) cc_final: 0.3053 (ttt) REVERT: D 171 GLN cc_start: 0.8595 (pt0) cc_final: 0.7088 (pm20) REVERT: D 242 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6959 (tm-30) REVERT: D 415 LEU cc_start: 0.8557 (pp) cc_final: 0.8356 (tt) REVERT: E 24 MET cc_start: 0.3040 (ttt) cc_final: 0.2603 (ttt) REVERT: E 202 GLN cc_start: 0.8171 (pm20) cc_final: 0.7490 (pm20) REVERT: E 415 LEU cc_start: 0.8621 (pp) cc_final: 0.8405 (tt) outliers start: 37 outliers final: 26 residues processed: 275 average time/residue: 0.2059 time to fit residues: 88.8797 Evaluate side-chains 256 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 1.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 14585 Z= 0.524 Angle : 1.266 14.886 19775 Z= 0.639 Chirality : 0.064 0.663 2265 Planarity : 0.008 0.087 2450 Dihedral : 7.768 56.189 2200 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.97 % Allowed : 23.10 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1710 helix: -1.29 (0.20), residues: 540 sheet: -1.36 (0.25), residues: 375 loop : -1.71 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 186 HIS 0.012 0.005 HIS E 125 PHE 0.036 0.004 PHE C 60 TYR 0.044 0.004 TYR D 218 ARG 0.026 0.002 ARG C 229 *********************** 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 294 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 248 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8166 (tp40) REVERT: A 173 GLU cc_start: 0.6706 (pm20) cc_final: 0.6460 (pm20) REVERT: A 202 GLN cc_start: 0.8553 (pm20) cc_final: 0.8141 (pm20) REVERT: B 83 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: C 202 GLN cc_start: 0.8923 (pm20) cc_final: 0.8468 (pm20) REVERT: D 24 MET cc_start: 0.6515 (ttt) cc_final: 0.4239 (ttt) REVERT: D 34 MET cc_start: 0.8824 (ptp) cc_final: 0.8608 (pmm) REVERT: D 236 MET cc_start: 0.7998 (mpp) cc_final: 0.7755 (mpp) REVERT: D 242 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7479 (tm-30) REVERT: E 24 MET cc_start: 0.6305 (ttt) cc_final: 0.3880 (ttt) REVERT: E 130 ASP cc_start: 0.8237 (p0) cc_final: 0.7744 (p0) REVERT: E 202 GLN cc_start: 0.8764 (pm20) cc_final: 0.8174 (pm20) outliers start: 46 outliers final: 24 residues processed: 279 average time/residue: 0.2485 time to fit residues: 102.2018 Evaluate side-chains 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 1.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14585 Z= 0.234 Angle : 0.946 15.775 19775 Z= 0.448 Chirality : 0.048 0.264 2265 Planarity : 0.004 0.045 2450 Dihedral : 6.471 48.651 2200 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.87 % Allowed : 25.35 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1710 helix: -0.70 (0.21), residues: 540 sheet: -1.05 (0.28), residues: 325 loop : -1.52 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 110 HIS 0.005 0.002 HIS E 217 PHE 0.025 0.002 PHE E 60 TYR 0.017 0.002 TYR E 218 ARG 0.008 0.001 ARG C 229 *********************** 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 263 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8543 (pm20) cc_final: 0.8291 (pm20) REVERT: A 242 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 59 ILE cc_start: 0.9169 (mp) cc_final: 0.8857 (mm) REVERT: B 242 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 202 GLN cc_start: 0.8870 (pm20) cc_final: 0.8478 (pm20) REVERT: D 24 MET cc_start: 0.5899 (ttt) cc_final: 0.4990 (ttt) REVERT: E 24 MET cc_start: 0.5624 (ttt) cc_final: 0.5184 (ttt) REVERT: E 69 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7408 (mm-30) REVERT: E 119 GLU cc_start: 0.7986 (tt0) cc_final: 0.7612 (tt0) REVERT: E 202 GLN cc_start: 0.8699 (pm20) cc_final: 0.8190 (pm20) REVERT: E 287 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7677 (ptp90) outliers start: 29 outliers final: 21 residues processed: 251 average time/residue: 0.2265 time to fit residues: 86.3746 Evaluate side-chains 214 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 1.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14585 Z= 0.283 Angle : 0.914 14.550 19775 Z= 0.440 Chirality : 0.048 0.227 2265 Planarity : 0.005 0.040 2450 Dihedral : 6.050 37.613 2200 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.61 % Allowed : 25.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1710 helix: -0.42 (0.23), residues: 540 sheet: -0.53 (0.28), residues: 355 loop : -1.68 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 84 HIS 0.015 0.003 HIS B 217 PHE 0.030 0.002 PHE A 60 TYR 0.027 0.002 TYR C 218 ARG 0.006 0.001 ARG A 88 ********************** 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 221 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.674 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 151 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8390 (m) REVERT: A 202 GLN cc_start: 0.8593 (pm20) cc_final: 0.8199 (pm20) REVERT: A 242 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 24 MET cc_start: 0.5714 (tmm) cc_final: 0.5212 (tmm) REVERT: B 202 GLN cc_start: 0.8462 (mp10) cc_final: 0.8239 (mp10) REVERT: B 242 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 262 MET cc_start: 0.1356 (mmm) cc_final: 0.0966 (tpt) REVERT: C 24 MET cc_start: 0.4977 (tmm) cc_final: 0.4749 (tmm) REVERT: D 218 TYR cc_start: 0.5319 (t80) cc_final: 0.4516 (t80) REVERT: E 24 MET cc_start: 0.5664 (ttt) cc_final: 0.4967 (ttt) REVERT: E 119 GLU cc_start: 0.8289 (tt0) cc_final: 0.7826 (tt0) outliers start: 25 outliers final: 17 residues processed: 212 average time/residue: 0.2302 time to fit residues: 74.2789 Evaluate side-chains 203 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 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 = 0.3931 r_free = 0.3931 target = 0.104647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079975 restraints weight = 50381.604| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 6.63 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 1.8037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14585 Z= 0.203 Angle : 0.874 13.880 19775 Z= 0.415 Chirality : 0.048 0.247 2265 Planarity : 0.004 0.047 2450 Dihedral : 5.660 38.717 2200 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.16 % Allowed : 26.71 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1710 helix: -0.11 (0.23), residues: 540 sheet: -0.23 (0.29), residues: 355 loop : -1.64 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 84 HIS 0.004 0.001 HIS C 217 PHE 0.028 0.002 PHE E 60 TYR 0.025 0.002 TYR B 218 ARG 0.008 0.001 ARG C 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.68 seconds wall clock time: 54 minutes 34.57 seconds (3274.57 seconds total)