Starting phenix.real_space_refine on Sun Nov 17 21:16:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/11_2024/8jaj_36127.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 216 5.16 5 C 30132 2.51 5 N 7968 2.21 5 O 9348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47664 Number of models: 1 Model: "" Number of chains: 1 Chain: "a" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3972 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 498} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: c, b, e, d, g, f, i, h, k, j, l Time building chain proxies: 12.50, per 1000 atoms: 0.26 Number of scatterers: 47664 At special positions: 0 Unit cell: (286.96, 289.68, 84.32, 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 216 16.00 O 9348 8.00 N 7968 7.00 C 30132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 11.13 Conformation dependent library (CDL) restraints added in 6.2 seconds 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11640 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 78 sheets defined 26.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'a' and resid 59 through 65 Processing helix chain 'a' and resid 76 through 86 Processing helix chain 'a' and resid 201 through 210 Processing helix chain 'a' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE a 222 " --> pdb=" O GLU a 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 219 through 222' Processing helix chain 'a' and resid 247 through 260 Processing helix chain 'a' and resid 275 through 290 Processing helix chain 'a' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU a 307 " --> pdb=" O TYR a 303 " (cutoff:3.500A) Proline residue: a 308 - end of helix removed outlier: 3.613A pdb=" N GLU a 311 " --> pdb=" O LEU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 358 Processing helix chain 'a' and resid 393 through 400 Processing helix chain 'a' and resid 431 through 451 removed outlier: 3.854A pdb=" N SER a 435 " --> pdb=" O GLN a 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU a 436 " --> pdb=" O HIS a 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN a 450 " --> pdb=" O GLN a 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET a 451 " --> pdb=" O LEU a 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 457 through 478 Processing helix chain 'b' and resid 59 through 65 Processing helix chain 'b' and resid 76 through 86 Processing helix chain 'b' and resid 201 through 210 Processing helix chain 'b' and resid 219 through 222 removed outlier: 3.722A pdb=" N ILE b 222 " --> pdb=" O GLU b 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 219 through 222' Processing helix chain 'b' and resid 247 through 260 Processing helix chain 'b' and resid 275 through 290 Processing helix chain 'b' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU b 307 " --> pdb=" O TYR b 303 " (cutoff:3.500A) Proline residue: b 308 - end of helix removed outlier: 3.613A pdb=" N GLU b 311 " --> pdb=" O LEU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 358 Processing helix chain 'b' and resid 393 through 400 Processing helix chain 'b' and resid 431 through 451 removed outlier: 3.854A pdb=" N SER b 435 " --> pdb=" O GLN b 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU b 436 " --> pdb=" O HIS b 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN b 450 " --> pdb=" O GLN b 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET b 451 " --> pdb=" O LEU b 447 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 478 Processing helix chain 'c' and resid 59 through 65 Processing helix chain 'c' and resid 76 through 86 Processing helix chain 'c' and resid 201 through 210 Processing helix chain 'c' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE c 222 " --> pdb=" O GLU c 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 219 through 222' Processing helix chain 'c' and resid 247 through 260 Processing helix chain 'c' and resid 275 through 290 Processing helix chain 'c' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU c 307 " --> pdb=" O TYR c 303 " (cutoff:3.500A) Proline residue: c 308 - end of helix removed outlier: 3.613A pdb=" N GLU c 311 " --> pdb=" O LEU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 347 through 358 Processing helix chain 'c' and resid 393 through 400 Processing helix chain 'c' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER c 435 " --> pdb=" O GLN c 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU c 436 " --> pdb=" O HIS c 432 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN c 450 " --> pdb=" O GLN c 446 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET c 451 " --> pdb=" O LEU c 447 " (cutoff:3.500A) Processing helix chain 'c' and resid 457 through 478 Processing helix chain 'd' and resid 59 through 65 Processing helix chain 'd' and resid 76 through 86 Processing helix chain 'd' and resid 201 through 210 Processing helix chain 'd' and resid 219 through 222 removed outlier: 3.722A pdb=" N ILE d 222 " --> pdb=" O GLU d 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 219 through 222' Processing helix chain 'd' and resid 247 through 260 Processing helix chain 'd' and resid 275 through 290 Processing helix chain 'd' and resid 302 through 313 removed outlier: 4.292A pdb=" N LEU d 307 " --> pdb=" O TYR d 303 " (cutoff:3.500A) Proline residue: d 308 - end of helix removed outlier: 3.613A pdb=" N GLU d 311 " --> pdb=" O LEU d 307 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 358 Processing helix chain 'd' and resid 393 through 400 Processing helix chain 'd' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER d 435 " --> pdb=" O GLN d 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU d 436 " --> pdb=" O HIS d 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN d 450 " --> pdb=" O GLN d 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET d 451 " --> pdb=" O LEU d 447 " (cutoff:3.500A) Processing helix chain 'd' and resid 457 through 478 Processing helix chain 'e' and resid 59 through 65 Processing helix chain 'e' and resid 76 through 86 Processing helix chain 'e' and resid 201 through 210 Processing helix chain 'e' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE e 222 " --> pdb=" O GLU e 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 219 through 222' Processing helix chain 'e' and resid 247 through 260 Processing helix chain 'e' and resid 275 through 290 Processing helix chain 'e' and resid 302 through 313 removed outlier: 4.292A pdb=" N LEU e 307 " --> pdb=" O TYR e 303 " (cutoff:3.500A) Proline residue: e 308 - end of helix removed outlier: 3.613A pdb=" N GLU e 311 " --> pdb=" O LEU e 307 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 358 Processing helix chain 'e' and resid 393 through 400 Processing helix chain 'e' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER e 435 " --> pdb=" O GLN e 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU e 436 " --> pdb=" O HIS e 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN e 450 " --> pdb=" O GLN e 446 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET e 451 " --> pdb=" O LEU e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 478 Processing helix chain 'f' and resid 59 through 65 Processing helix chain 'f' and resid 76 through 86 Processing helix chain 'f' and resid 201 through 210 Processing helix chain 'f' and resid 219 through 222 removed outlier: 3.722A pdb=" N ILE f 222 " --> pdb=" O GLU f 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 219 through 222' Processing helix chain 'f' and resid 247 through 260 Processing helix chain 'f' and resid 275 through 290 Processing helix chain 'f' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU f 307 " --> pdb=" O TYR f 303 " (cutoff:3.500A) Proline residue: f 308 - end of helix removed outlier: 3.612A pdb=" N GLU f 311 " --> pdb=" O LEU f 307 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 358 Processing helix chain 'f' and resid 393 through 400 Processing helix chain 'f' and resid 431 through 451 removed outlier: 3.854A pdb=" N SER f 435 " --> pdb=" O GLN f 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU f 436 " --> pdb=" O HIS f 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN f 450 " --> pdb=" O GLN f 446 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET f 451 " --> pdb=" O LEU f 447 " (cutoff:3.500A) Processing helix chain 'f' and resid 457 through 478 Processing helix chain 'g' and resid 59 through 65 Processing helix chain 'g' and resid 76 through 86 Processing helix chain 'g' and resid 201 through 210 Processing helix chain 'g' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE g 222 " --> pdb=" O GLU g 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 219 through 222' Processing helix chain 'g' and resid 247 through 260 Processing helix chain 'g' and resid 275 through 290 Processing helix chain 'g' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Proline residue: g 308 - end of helix removed outlier: 3.614A pdb=" N GLU g 311 " --> pdb=" O LEU g 307 " (cutoff:3.500A) Processing helix chain 'g' and resid 347 through 358 Processing helix chain 'g' and resid 393 through 400 Processing helix chain 'g' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER g 435 " --> pdb=" O GLN g 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU g 436 " --> pdb=" O HIS g 432 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN g 450 " --> pdb=" O GLN g 446 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET g 451 " --> pdb=" O LEU g 447 " (cutoff:3.500A) Processing helix chain 'g' and resid 457 through 478 Processing helix chain 'h' and resid 59 through 65 Processing helix chain 'h' and resid 76 through 86 Processing helix chain 'h' and resid 201 through 210 Processing helix chain 'h' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE h 222 " --> pdb=" O GLU h 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 219 through 222' Processing helix chain 'h' and resid 247 through 260 Processing helix chain 'h' and resid 275 through 290 Processing helix chain 'h' and resid 302 through 313 removed outlier: 4.292A pdb=" N LEU h 307 " --> pdb=" O TYR h 303 " (cutoff:3.500A) Proline residue: h 308 - end of helix removed outlier: 3.613A pdb=" N GLU h 311 " --> pdb=" O LEU h 307 " (cutoff:3.500A) Processing helix chain 'h' and resid 347 through 358 Processing helix chain 'h' and resid 393 through 400 Processing helix chain 'h' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER h 435 " --> pdb=" O GLN h 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU h 436 " --> pdb=" O HIS h 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN h 450 " --> pdb=" O GLN h 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET h 451 " --> pdb=" O LEU h 447 " (cutoff:3.500A) Processing helix chain 'h' and resid 457 through 478 Processing helix chain 'i' and resid 59 through 65 Processing helix chain 'i' and resid 76 through 86 Processing helix chain 'i' and resid 201 through 210 Processing helix chain 'i' and resid 219 through 222 removed outlier: 3.722A pdb=" N ILE i 222 " --> pdb=" O GLU i 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 219 through 222' Processing helix chain 'i' and resid 247 through 260 Processing helix chain 'i' and resid 275 through 290 Processing helix chain 'i' and resid 302 through 313 removed outlier: 4.292A pdb=" N LEU i 307 " --> pdb=" O TYR i 303 " (cutoff:3.500A) Proline residue: i 308 - end of helix removed outlier: 3.613A pdb=" N GLU i 311 " --> pdb=" O LEU i 307 " (cutoff:3.500A) Processing helix chain 'i' and resid 347 through 358 Processing helix chain 'i' and resid 393 through 400 Processing helix chain 'i' and resid 431 through 451 removed outlier: 3.854A pdb=" N SER i 435 " --> pdb=" O GLN i 431 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU i 436 " --> pdb=" O HIS i 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN i 450 " --> pdb=" O GLN i 446 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET i 451 " --> pdb=" O LEU i 447 " (cutoff:3.500A) Processing helix chain 'i' and resid 457 through 478 Processing helix chain 'j' and resid 59 through 65 Processing helix chain 'j' and resid 76 through 86 Processing helix chain 'j' and resid 201 through 210 Processing helix chain 'j' and resid 219 through 222 removed outlier: 3.722A pdb=" N ILE j 222 " --> pdb=" O GLU j 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 219 through 222' Processing helix chain 'j' and resid 247 through 260 removed outlier: 3.501A pdb=" N ASN j 260 " --> pdb=" O LYS j 256 " (cutoff:3.500A) Processing helix chain 'j' and resid 275 through 290 Processing helix chain 'j' and resid 302 through 313 removed outlier: 4.294A pdb=" N LEU j 307 " --> pdb=" O TYR j 303 " (cutoff:3.500A) Proline residue: j 308 - end of helix removed outlier: 3.613A pdb=" N GLU j 311 " --> pdb=" O LEU j 307 " (cutoff:3.500A) Processing helix chain 'j' and resid 347 through 358 Processing helix chain 'j' and resid 393 through 400 Processing helix chain 'j' and resid 431 through 451 removed outlier: 3.854A pdb=" N SER j 435 " --> pdb=" O GLN j 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU j 436 " --> pdb=" O HIS j 432 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN j 450 " --> pdb=" O GLN j 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET j 451 " --> pdb=" O LEU j 447 " (cutoff:3.500A) Processing helix chain 'j' and resid 457 through 478 Processing helix chain 'k' and resid 59 through 65 Processing helix chain 'k' and resid 76 through 86 Processing helix chain 'k' and resid 201 through 210 Processing helix chain 'k' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE k 222 " --> pdb=" O GLU k 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 219 through 222' Processing helix chain 'k' and resid 247 through 260 removed outlier: 3.500A pdb=" N ASN k 260 " --> pdb=" O LYS k 256 " (cutoff:3.500A) Processing helix chain 'k' and resid 275 through 290 Processing helix chain 'k' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU k 307 " --> pdb=" O TYR k 303 " (cutoff:3.500A) Proline residue: k 308 - end of helix removed outlier: 3.613A pdb=" N GLU k 311 " --> pdb=" O LEU k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 347 through 358 Processing helix chain 'k' and resid 393 through 400 Processing helix chain 'k' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER k 435 " --> pdb=" O GLN k 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU k 436 " --> pdb=" O HIS k 432 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN k 450 " --> pdb=" O GLN k 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET k 451 " --> pdb=" O LEU k 447 " (cutoff:3.500A) Processing helix chain 'k' and resid 457 through 478 Processing helix chain 'l' and resid 59 through 65 Processing helix chain 'l' and resid 76 through 86 Processing helix chain 'l' and resid 201 through 210 Processing helix chain 'l' and resid 219 through 222 removed outlier: 3.721A pdb=" N ILE l 222 " --> pdb=" O GLU l 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 219 through 222' Processing helix chain 'l' and resid 247 through 260 removed outlier: 3.500A pdb=" N ASN l 260 " --> pdb=" O LYS l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 275 through 290 Processing helix chain 'l' and resid 302 through 313 removed outlier: 4.293A pdb=" N LEU l 307 " --> pdb=" O TYR l 303 " (cutoff:3.500A) Proline residue: l 308 - end of helix removed outlier: 3.614A pdb=" N GLU l 311 " --> pdb=" O LEU l 307 " (cutoff:3.500A) Processing helix chain 'l' and resid 347 through 358 Processing helix chain 'l' and resid 393 through 400 Processing helix chain 'l' and resid 431 through 451 removed outlier: 3.853A pdb=" N SER l 435 " --> pdb=" O GLN l 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU l 436 " --> pdb=" O HIS l 432 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN l 450 " --> pdb=" O GLN l 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET l 451 " --> pdb=" O LEU l 447 " (cutoff:3.500A) Processing helix chain 'l' and resid 457 through 478 Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 18 removed outlier: 6.941A pdb=" N ALA a 17 " --> pdb=" O GLY b 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.087A pdb=" N ALA a 39 " --> pdb=" O LEU a 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL a 268 " --> pdb=" O PHE a 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP a 296 " --> pdb=" O VAL a 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 114 through 120 removed outlier: 3.936A pdb=" N VAL a 137 " --> pdb=" O PRO a 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 178 through 187 removed outlier: 5.560A pdb=" N THR a 180 " --> pdb=" O GLN a 171 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN a 171 " --> pdb=" O THR a 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE a 152 " --> pdb=" O LYS a 231 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS a 231 " --> pdb=" O ILE a 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 332 through 333 Processing sheet with id=AA6, first strand: chain 'a' and resid 405 through 407 Processing sheet with id=AA7, first strand: chain 'a' and resid 494 through 499 removed outlier: 6.102A pdb=" N TRP a 506 " --> pdb=" O GLN g 522 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL g 524 " --> pdb=" O TRP a 506 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL a 508 " --> pdb=" O VAL g 524 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU g 526 " --> pdb=" O VAL a 508 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP a 510 " --> pdb=" O LEU g 526 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE g 521 " --> pdb=" O ALA l 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 522 through 523 removed outlier: 3.690A pdb=" N GLY a 523 " --> pdb=" O ALA f 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'b' and resid 17 through 18 removed outlier: 6.888A pdb=" N ALA b 17 " --> pdb=" O GLY c 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'b' and resid 52 through 55 removed outlier: 6.088A pdb=" N ALA b 39 " --> pdb=" O LEU b 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL b 268 " --> pdb=" O PHE b 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP b 296 " --> pdb=" O VAL b 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 114 through 120 removed outlier: 3.936A pdb=" N VAL b 137 " --> pdb=" O PRO b 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR b 180 " --> pdb=" O GLN b 171 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN b 171 " --> pdb=" O THR b 180 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE b 152 " --> pdb=" O LYS b 231 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS b 231 " --> pdb=" O ILE b 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'b' and resid 405 through 407 Processing sheet with id=AB6, first strand: chain 'b' and resid 494 through 499 removed outlier: 6.120A pdb=" N TRP b 506 " --> pdb=" O GLN h 522 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL h 524 " --> pdb=" O TRP b 506 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL b 508 " --> pdb=" O VAL h 524 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU h 526 " --> pdb=" O VAL b 508 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP b 510 " --> pdb=" O LEU h 526 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA g 17 " --> pdb=" O ILE h 521 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY h 523 " --> pdb=" O ALA g 17 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 17 through 18 removed outlier: 6.990A pdb=" N ALA c 17 " --> pdb=" O GLY d 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'c' and resid 52 through 55 removed outlier: 6.087A pdb=" N ALA c 39 " --> pdb=" O LEU c 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL c 268 " --> pdb=" O PHE c 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP c 296 " --> pdb=" O VAL c 268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL c 137 " --> pdb=" O PRO c 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 178 through 187 removed outlier: 5.560A pdb=" N THR c 180 " --> pdb=" O GLN c 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN c 171 " --> pdb=" O THR c 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE c 152 " --> pdb=" O LYS c 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS c 231 " --> pdb=" O ILE c 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 332 through 333 Processing sheet with id=AC3, first strand: chain 'c' and resid 405 through 407 Processing sheet with id=AC4, first strand: chain 'c' and resid 494 through 499 removed outlier: 6.115A pdb=" N TRP c 506 " --> pdb=" O GLN i 522 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL i 524 " --> pdb=" O TRP c 506 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL c 508 " --> pdb=" O VAL i 524 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU i 526 " --> pdb=" O VAL c 508 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TRP c 510 " --> pdb=" O LEU i 526 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA h 17 " --> pdb=" O ILE i 521 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY i 523 " --> pdb=" O ALA h 17 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 17 through 18 removed outlier: 6.913A pdb=" N ALA d 17 " --> pdb=" O GLY e 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'd' and resid 52 through 55 removed outlier: 6.086A pdb=" N ALA d 39 " --> pdb=" O LEU d 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL d 268 " --> pdb=" O PHE d 294 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP d 296 " --> pdb=" O VAL d 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 114 through 120 removed outlier: 3.936A pdb=" N VAL d 137 " --> pdb=" O PRO d 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR d 180 " --> pdb=" O GLN d 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN d 171 " --> pdb=" O THR d 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE d 152 " --> pdb=" O LYS d 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS d 231 " --> pdb=" O ILE d 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 332 through 333 Processing sheet with id=AD1, first strand: chain 'd' and resid 405 through 407 Processing sheet with id=AD2, first strand: chain 'd' and resid 494 through 499 removed outlier: 6.112A pdb=" N TRP d 506 " --> pdb=" O GLN j 522 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL j 524 " --> pdb=" O TRP d 506 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL d 508 " --> pdb=" O VAL j 524 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU j 526 " --> pdb=" O VAL d 508 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP d 510 " --> pdb=" O LEU j 526 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA i 17 " --> pdb=" O ILE j 521 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY j 523 " --> pdb=" O ALA i 17 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 17 through 18 removed outlier: 6.921A pdb=" N ALA e 17 " --> pdb=" O GLY f 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'e' and resid 52 through 55 removed outlier: 6.088A pdb=" N ALA e 39 " --> pdb=" O LEU e 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL e 268 " --> pdb=" O PHE e 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP e 296 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL e 137 " --> pdb=" O PRO e 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 178 through 187 removed outlier: 5.559A pdb=" N THR e 180 " --> pdb=" O GLN e 171 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN e 171 " --> pdb=" O THR e 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE e 152 " --> pdb=" O LYS e 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS e 231 " --> pdb=" O ILE e 152 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 332 through 333 Processing sheet with id=AD8, first strand: chain 'e' and resid 405 through 407 Processing sheet with id=AD9, first strand: chain 'e' and resid 494 through 499 removed outlier: 6.111A pdb=" N TRP e 506 " --> pdb=" O GLN k 522 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL k 524 " --> pdb=" O TRP e 506 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL e 508 " --> pdb=" O VAL k 524 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU k 526 " --> pdb=" O VAL e 508 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TRP e 510 " --> pdb=" O LEU k 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA j 17 " --> pdb=" O ILE k 521 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY k 523 " --> pdb=" O ALA j 17 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 52 through 55 removed outlier: 6.087A pdb=" N ALA f 39 " --> pdb=" O LEU f 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL f 268 " --> pdb=" O PHE f 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP f 296 " --> pdb=" O VAL f 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'f' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL f 137 " --> pdb=" O PRO f 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR f 180 " --> pdb=" O GLN f 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN f 171 " --> pdb=" O THR f 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE f 152 " --> pdb=" O LYS f 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS f 231 " --> pdb=" O ILE f 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 332 through 333 Processing sheet with id=AE5, first strand: chain 'f' and resid 405 through 407 Processing sheet with id=AE6, first strand: chain 'f' and resid 494 through 499 removed outlier: 6.243A pdb=" N TRP f 506 " --> pdb=" O GLN l 522 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL l 524 " --> pdb=" O TRP f 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL f 508 " --> pdb=" O VAL l 524 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU l 526 " --> pdb=" O VAL f 508 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP f 510 " --> pdb=" O LEU l 526 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA k 17 " --> pdb=" O ILE l 521 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY l 523 " --> pdb=" O ALA k 17 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 52 through 55 removed outlier: 6.088A pdb=" N ALA g 39 " --> pdb=" O LEU g 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL g 268 " --> pdb=" O PHE g 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP g 296 " --> pdb=" O VAL g 268 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 114 through 120 removed outlier: 3.934A pdb=" N VAL g 137 " --> pdb=" O PRO g 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'g' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR g 180 " --> pdb=" O GLN g 171 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN g 171 " --> pdb=" O THR g 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE g 152 " --> pdb=" O LYS g 231 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS g 231 " --> pdb=" O ILE g 152 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 332 through 333 Processing sheet with id=AF2, first strand: chain 'g' and resid 405 through 407 Processing sheet with id=AF3, first strand: chain 'g' and resid 494 through 499 Processing sheet with id=AF4, first strand: chain 'h' and resid 52 through 55 removed outlier: 6.088A pdb=" N ALA h 39 " --> pdb=" O LEU h 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL h 268 " --> pdb=" O PHE h 294 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP h 296 " --> pdb=" O VAL h 268 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL h 137 " --> pdb=" O PRO h 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 178 through 187 removed outlier: 5.560A pdb=" N THR h 180 " --> pdb=" O GLN h 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN h 171 " --> pdb=" O THR h 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE h 152 " --> pdb=" O LYS h 231 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS h 231 " --> pdb=" O ILE h 152 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 332 through 333 Processing sheet with id=AF8, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AF9, first strand: chain 'h' and resid 494 through 499 Processing sheet with id=AG1, first strand: chain 'i' and resid 52 through 55 removed outlier: 6.088A pdb=" N ALA i 39 " --> pdb=" O LEU i 269 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL i 268 " --> pdb=" O PHE i 294 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP i 296 " --> pdb=" O VAL i 268 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'i' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL i 137 " --> pdb=" O PRO i 104 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 178 through 187 removed outlier: 5.560A pdb=" N THR i 180 " --> pdb=" O GLN i 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN i 171 " --> pdb=" O THR i 180 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE i 152 " --> pdb=" O LYS i 231 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS i 231 " --> pdb=" O ILE i 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 332 through 333 Processing sheet with id=AG5, first strand: chain 'i' and resid 405 through 407 Processing sheet with id=AG6, first strand: chain 'i' and resid 494 through 499 Processing sheet with id=AG7, first strand: chain 'j' and resid 52 through 55 removed outlier: 6.087A pdb=" N ALA j 39 " --> pdb=" O LEU j 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL j 268 " --> pdb=" O PHE j 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP j 296 " --> pdb=" O VAL j 268 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'j' and resid 114 through 120 removed outlier: 3.936A pdb=" N VAL j 137 " --> pdb=" O PRO j 104 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR j 180 " --> pdb=" O GLN j 171 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN j 171 " --> pdb=" O THR j 180 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE j 152 " --> pdb=" O LYS j 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS j 231 " --> pdb=" O ILE j 152 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 332 through 333 Processing sheet with id=AH2, first strand: chain 'j' and resid 405 through 407 Processing sheet with id=AH3, first strand: chain 'j' and resid 494 through 499 Processing sheet with id=AH4, first strand: chain 'k' and resid 52 through 55 removed outlier: 6.086A pdb=" N ALA k 39 " --> pdb=" O LEU k 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL k 268 " --> pdb=" O PHE k 294 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP k 296 " --> pdb=" O VAL k 268 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'k' and resid 114 through 120 removed outlier: 3.935A pdb=" N VAL k 137 " --> pdb=" O PRO k 104 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'k' and resid 178 through 187 removed outlier: 5.561A pdb=" N THR k 180 " --> pdb=" O GLN k 171 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN k 171 " --> pdb=" O THR k 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE k 152 " --> pdb=" O LYS k 231 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS k 231 " --> pdb=" O ILE k 152 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'k' and resid 332 through 333 Processing sheet with id=AH8, first strand: chain 'k' and resid 405 through 407 Processing sheet with id=AH9, first strand: chain 'k' and resid 494 through 499 Processing sheet with id=AI1, first strand: chain 'l' and resid 52 through 55 removed outlier: 6.087A pdb=" N ALA l 39 " --> pdb=" O LEU l 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL l 268 " --> pdb=" O PHE l 294 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASP l 296 " --> pdb=" O VAL l 268 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'l' and resid 114 through 120 removed outlier: 3.936A pdb=" N VAL l 137 " --> pdb=" O PRO l 104 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'l' and resid 178 through 187 removed outlier: 5.560A pdb=" N THR l 180 " --> pdb=" O GLN l 171 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN l 171 " --> pdb=" O THR l 180 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE l 152 " --> pdb=" O LYS l 231 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS l 231 " --> pdb=" O ILE l 152 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'l' and resid 332 through 333 Processing sheet with id=AI5, first strand: chain 'l' and resid 405 through 407 Processing sheet with id=AI6, first strand: chain 'l' and resid 494 through 499 1617 hydrogen bonds defined for protein. 4725 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: 19.55 Time building geometry restraints manager: 13.32 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: 15732 1.34 - 1.46: 10311 1.46 - 1.58: 22293 1.58 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 48648 Sorted by residual: bond pdb=" C SER l 145 " pdb=" N PRO l 146 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.93e+00 bond pdb=" C SER e 145 " pdb=" N PRO e 146 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.93e+00 bond pdb=" C SER k 145 " pdb=" N PRO k 146 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.92e+00 bond pdb=" C SER g 145 " pdb=" N PRO g 146 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.91e+00 bond pdb=" C SER d 145 " pdb=" N PRO d 146 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 ... (remaining 48643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 63890 1.11 - 2.23: 1773 2.23 - 3.34: 462 3.34 - 4.46: 60 4.46 - 5.57: 67 Bond angle restraints: 66252 Sorted by residual: angle pdb=" N ASN i 34 " pdb=" CA ASN i 34 " pdb=" C ASN i 34 " ideal model delta sigma weight residual 114.56 110.56 4.00 1.27e+00 6.20e-01 9.91e+00 angle pdb=" N ASN g 34 " pdb=" CA ASN g 34 " pdb=" C ASN g 34 " ideal model delta sigma weight residual 114.56 110.59 3.97 1.27e+00 6.20e-01 9.77e+00 angle pdb=" N ASN h 34 " pdb=" CA ASN h 34 " pdb=" C ASN h 34 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.69e+00 angle pdb=" N ASN f 34 " pdb=" CA ASN f 34 " pdb=" C ASN f 34 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.66e+00 angle pdb=" N ASN k 34 " pdb=" CA ASN k 34 " pdb=" C ASN k 34 " ideal model delta sigma weight residual 114.56 110.61 3.95 1.27e+00 6.20e-01 9.66e+00 ... (remaining 66247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 26964 17.96 - 35.92: 1812 35.92 - 53.88: 252 53.88 - 71.84: 84 71.84 - 89.80: 24 Dihedral angle restraints: 29136 sinusoidal: 10932 harmonic: 18204 Sorted by residual: dihedral pdb=" CA SER l 145 " pdb=" C SER l 145 " pdb=" N PRO l 146 " pdb=" CA PRO l 146 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER b 145 " pdb=" C SER b 145 " pdb=" N PRO b 146 " pdb=" CA PRO b 146 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER g 145 " pdb=" C SER g 145 " pdb=" N PRO g 146 " pdb=" CA PRO g 146 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 29133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4847 0.028 - 0.055: 1645 0.055 - 0.083: 549 0.083 - 0.110: 465 0.110 - 0.138: 138 Chirality restraints: 7644 Sorted by residual: chirality pdb=" CA ILE b 105 " pdb=" N ILE b 105 " pdb=" C ILE b 105 " pdb=" CB ILE b 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE j 105 " pdb=" N ILE j 105 " pdb=" C ILE j 105 " pdb=" CB ILE j 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE f 105 " pdb=" N ILE f 105 " pdb=" C ILE f 105 " pdb=" CB ILE f 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 7641 not shown) Planarity restraints: 8592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER k 145 " -0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO k 146 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO k 146 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO k 146 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER e 145 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO e 146 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO e 146 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO e 146 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER f 145 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO f 146 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO f 146 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO f 146 " -0.047 5.00e-02 4.00e+02 ... (remaining 8589 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 427 2.63 - 3.20: 41663 3.20 - 3.77: 67908 3.77 - 4.33: 90753 4.33 - 4.90: 155016 Nonbonded interactions: 355767 Sorted by model distance: nonbonded pdb=" ND2 ASN a 426 " pdb=" O ALA l 23 " model vdw 2.064 3.120 nonbonded pdb=" ND2 ASN c 426 " pdb=" O ALA h 23 " model vdw 2.073 3.120 nonbonded pdb=" ND2 ASN e 426 " pdb=" O ALA j 23 " model vdw 2.110 3.120 nonbonded pdb=" ND2 ASN d 426 " pdb=" O ALA i 23 " model vdw 2.127 3.120 nonbonded pdb=" ND2 ASN f 426 " pdb=" O ALA k 23 " model vdw 2.128 3.120 ... (remaining 355762 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' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.740 Check model and map are aligned: 0.330 Set scattering table: 0.470 Process input model: 87.640 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 0.039 48648 Z= 0.140 Angle : 0.509 5.572 66252 Z= 0.286 Chirality : 0.040 0.138 7644 Planarity : 0.004 0.084 8592 Dihedral : 12.657 89.804 17496 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.24 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.70 (0.10), residues: 6288 helix: 2.41 (0.14), residues: 1524 sheet: 2.02 (0.16), residues: 1056 loop : -0.93 (0.10), residues: 3708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 506 HIS 0.003 0.001 HIS d 367 PHE 0.006 0.001 PHE d 103 TYR 0.007 0.001 TYR f 350 ARG 0.003 0.000 ARG l 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 5.220 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 outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.5579 time to fit residues: 516.9140 Evaluate side-chains 186 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 5.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 6.9990 chunk 472 optimal weight: 10.0000 chunk 262 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 30.0000 chunk 189 optimal weight: 5.9990 chunk 297 optimal weight: 0.1980 chunk 364 optimal weight: 20.0000 chunk 566 optimal weight: 20.0000 overall best weight: 6.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 453 HIS ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 384 GLN g 522 GLN h 384 GLN i 384 GLN j 384 GLN k 384 GLN l 384 GLN l 429 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 48648 Z= 0.279 Angle : 0.651 11.565 66252 Z= 0.340 Chirality : 0.045 0.149 7644 Planarity : 0.006 0.085 8592 Dihedral : 4.503 22.154 6816 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.10 % Favored : 95.64 % Rotamer: Outliers : 1.00 % Allowed : 6.49 % Favored : 92.51 % 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: 0.26 (0.10), residues: 6288 helix: 1.57 (0.13), residues: 1560 sheet: 2.00 (0.17), residues: 936 loop : -0.97 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP j 506 HIS 0.004 0.001 HIS f 453 PHE 0.019 0.002 PHE a 343 TYR 0.019 0.002 TYR e 83 ARG 0.005 0.001 ARG a 380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 5.286 Fit side-chains revert: symmetry clash REVERT: d 264 MET cc_start: 0.8274 (tmm) cc_final: 0.7751 (tmm) REVERT: g 437 MET cc_start: 0.8447 (mmp) cc_final: 0.8067 (mmp) REVERT: j 437 MET cc_start: 0.8391 (mmp) cc_final: 0.8156 (mmp) REVERT: j 451 MET cc_start: 0.6746 (mmp) cc_final: 0.6325 (mmp) REVERT: k 432 HIS cc_start: 0.6286 (t70) cc_final: 0.6041 (t70) REVERT: k 467 MET cc_start: 0.7701 (mmm) cc_final: 0.7299 (tpp) REVERT: l 264 MET cc_start: 0.6758 (tpp) cc_final: 0.6460 (tpp) outliers start: 51 outliers final: 26 residues processed: 230 average time/residue: 0.5433 time to fit residues: 218.7022 Evaluate side-chains 160 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 195 ASP Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain e residue 195 ASP Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain g residue 236 THR Chi-restraints excluded: chain g residue 323 CYS Chi-restraints excluded: chain g residue 453 HIS Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 343 PHE Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 236 THR Chi-restraints excluded: chain i residue 323 CYS Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 236 THR Chi-restraints excluded: chain j residue 323 CYS Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 323 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 323 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 385 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 567 optimal weight: 10.0000 chunk 613 optimal weight: 5.9990 chunk 505 optimal weight: 30.0000 chunk 562 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 522 GLN b 75 GLN ** b 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 522 GLN ** c 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 522 GLN d 75 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN e 75 GLN ** e 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN ** f 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 522 GLN ** g 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 432 HIS ** h 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 429 HIS h 432 HIS ** i 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 432 HIS i 500 GLN ** j 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 429 HIS ** j 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 522 GLN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 48648 Z= 0.454 Angle : 0.753 7.827 66252 Z= 0.400 Chirality : 0.048 0.161 7644 Planarity : 0.006 0.084 8592 Dihedral : 5.625 27.827 6816 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.52 % Favored : 95.15 % Rotamer: Outliers : 1.90 % Allowed : 10.73 % Favored : 87.37 % 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: -0.38 (0.10), residues: 6288 helix: 0.94 (0.13), residues: 1560 sheet: 1.49 (0.18), residues: 828 loop : -1.22 (0.09), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 506 HIS 0.008 0.001 HIS h 432 PHE 0.026 0.003 PHE l 474 TYR 0.024 0.002 TYR c 350 ARG 0.005 0.001 ARG i 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 140 time to evaluate : 5.217 Fit side-chains REVERT: b 397 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8540 (mtt) REVERT: c 264 MET cc_start: 0.8648 (tmm) cc_final: 0.8368 (tmm) REVERT: f 264 MET cc_start: 0.8645 (tmm) cc_final: 0.8365 (tmm) REVERT: g 343 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (m-10) REVERT: g 413 MET cc_start: 0.8386 (mmm) cc_final: 0.8012 (mmt) REVERT: h 264 MET cc_start: 0.7822 (tpp) cc_final: 0.7608 (tpp) REVERT: h 367 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.7008 (m170) REVERT: i 367 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6738 (m170) REVERT: j 343 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (m-10) REVERT: j 413 MET cc_start: 0.8421 (mmm) cc_final: 0.8178 (mmt) REVERT: k 367 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6964 (m170) REVERT: k 432 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7436 (t70) REVERT: k 467 MET cc_start: 0.8324 (mmm) cc_final: 0.8024 (mmp) REVERT: l 367 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6503 (m170) REVERT: l 432 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7686 (t70) outliers start: 97 outliers final: 43 residues processed: 226 average time/residue: 0.5050 time to fit residues: 206.4592 Evaluate side-chains 163 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 397 MET Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain c residue 222 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain d residue 343 PHE Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 397 MET Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain g residue 239 THR Chi-restraints excluded: chain g residue 323 CYS Chi-restraints excluded: chain g residue 343 PHE Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 343 PHE Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain i residue 82 VAL Chi-restraints excluded: chain i residue 125 ILE Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 236 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 323 CYS Chi-restraints excluded: chain i residue 367 HIS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 110 GLU Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 239 THR Chi-restraints excluded: chain j residue 323 CYS Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 323 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 432 HIS Chi-restraints excluded: chain k residue 441 SER Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 323 CYS Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 432 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 7.9990 chunk 426 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 381 optimal weight: 20.0000 chunk 569 optimal weight: 7.9990 chunk 603 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 539 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 218 ASN ** g 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 429 HIS h 432 HIS h 522 GLN i 432 HIS j 218 ASN j 429 HIS j 432 HIS j 522 GLN ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS l 522 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 48648 Z= 0.276 Angle : 0.587 10.182 66252 Z= 0.311 Chirality : 0.044 0.175 7644 Planarity : 0.005 0.089 8592 Dihedral : 5.097 24.640 6816 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.91 % Favored : 94.77 % Rotamer: Outliers : 1.78 % Allowed : 12.00 % Favored : 86.22 % 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: -0.34 (0.10), residues: 6288 helix: 1.09 (0.13), residues: 1572 sheet: 1.54 (0.19), residues: 804 loop : -1.24 (0.09), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP i 506 HIS 0.006 0.001 HIS h 432 PHE 0.015 0.002 PHE j 474 TYR 0.012 0.001 TYR l 350 ARG 0.004 0.000 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 127 time to evaluate : 5.184 Fit side-chains REVERT: a 196 MET cc_start: 0.8928 (mmm) cc_final: 0.8692 (mmt) REVERT: c 264 MET cc_start: 0.8543 (tmm) cc_final: 0.8208 (tmm) REVERT: c 437 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8894 (mmp) REVERT: d 196 MET cc_start: 0.8914 (mmm) cc_final: 0.8678 (mmt) REVERT: d 264 MET cc_start: 0.8684 (tmm) cc_final: 0.8263 (tmm) REVERT: d 367 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (m170) REVERT: f 264 MET cc_start: 0.8579 (tmm) cc_final: 0.8241 (tmm) REVERT: g 413 MET cc_start: 0.8402 (mmm) cc_final: 0.8082 (mmt) REVERT: i 526 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8458 (mt) REVERT: j 413 MET cc_start: 0.8378 (mmm) cc_final: 0.8173 (mmt) REVERT: k 432 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6447 (t70) REVERT: l 526 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8473 (mt) outliers start: 91 outliers final: 48 residues processed: 207 average time/residue: 0.5267 time to fit residues: 198.8768 Evaluate side-chains 174 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 5.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain c residue 222 ILE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 437 MET Chi-restraints excluded: chain d residue 217 VAL Chi-restraints excluded: chain d residue 367 HIS Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 397 MET Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain g residue 323 CYS Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 239 THR Chi-restraints excluded: chain h residue 302 THR Chi-restraints excluded: chain h residue 323 CYS Chi-restraints excluded: chain h residue 391 THR Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 125 ILE Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 323 CYS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain i residue 526 LEU Chi-restraints excluded: chain j residue 125 ILE Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 323 CYS Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 391 THR Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 239 THR Chi-restraints excluded: chain k residue 323 CYS Chi-restraints excluded: chain k residue 432 HIS Chi-restraints excluded: chain k residue 441 SER Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 323 CYS Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 449 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 514 optimal weight: 7.9990 chunk 416 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 541 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 432 HIS h 432 HIS i 432 HIS ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS l 432 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48648 Z= 0.288 Angle : 0.587 7.128 66252 Z= 0.311 Chirality : 0.044 0.159 7644 Planarity : 0.005 0.090 8592 Dihedral : 5.021 25.402 6816 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.99 % Favored : 94.55 % Rotamer: Outliers : 2.39 % Allowed : 12.12 % Favored : 85.49 % 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: -0.34 (0.10), residues: 6288 helix: 1.16 (0.13), residues: 1560 sheet: 1.38 (0.19), residues: 804 loop : -1.23 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 506 HIS 0.006 0.001 HIS b 432 PHE 0.016 0.002 PHE g 474 TYR 0.015 0.001 TYR e 350 ARG 0.005 0.000 ARG l 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 124 time to evaluate : 5.360 Fit side-chains REVERT: a 196 MET cc_start: 0.8930 (mmm) cc_final: 0.8719 (mmt) REVERT: a 264 MET cc_start: 0.8684 (tmm) cc_final: 0.8223 (tmm) REVERT: c 264 MET cc_start: 0.8590 (tmm) cc_final: 0.8257 (tmm) REVERT: d 196 MET cc_start: 0.8907 (mmm) cc_final: 0.8694 (mmt) REVERT: d 264 MET cc_start: 0.8716 (tmm) cc_final: 0.8292 (tmm) REVERT: d 367 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7685 (m170) REVERT: f 264 MET cc_start: 0.8598 (tmm) cc_final: 0.8260 (tmm) REVERT: g 413 MET cc_start: 0.8392 (mmm) cc_final: 0.8095 (mmt) REVERT: g 437 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7789 (mmm) REVERT: h 367 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.7100 (m170) REVERT: h 500 GLN cc_start: 0.5539 (tm-30) cc_final: 0.5273 (tm-30) REVERT: i 367 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6694 (m170) REVERT: j 343 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: k 367 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6998 (m170) REVERT: k 500 GLN cc_start: 0.5509 (tm-30) cc_final: 0.5245 (tm-30) REVERT: l 367 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6636 (m170) outliers start: 122 outliers final: 63 residues processed: 239 average time/residue: 0.4977 time to fit residues: 219.1449 Evaluate side-chains 185 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 115 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 343 PHE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain b residue 526 LEU Chi-restraints excluded: chain c residue 222 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 414 ILE Chi-restraints excluded: chain c residue 437 MET Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 217 VAL Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 343 PHE Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 367 HIS Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 397 MET Chi-restraints excluded: chain e residue 526 LEU Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 414 ILE Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain g residue 323 CYS Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 323 CYS Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 125 ILE Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 323 CYS Chi-restraints excluded: chain i residue 367 HIS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 125 ILE Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 323 CYS Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 391 THR Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 323 CYS Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 441 SER Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 125 ILE Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 510 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 8.9990 chunk 543 optimal weight: 40.0000 chunk 119 optimal weight: 40.0000 chunk 354 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 603 optimal weight: 20.0000 chunk 501 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 316 optimal weight: 1.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 432 HIS i 432 HIS j 432 HIS ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 48648 Z= 0.253 Angle : 0.568 6.762 66252 Z= 0.299 Chirality : 0.043 0.171 7644 Planarity : 0.005 0.090 8592 Dihedral : 4.897 24.184 6816 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.45 % Favored : 95.04 % Rotamer: Outliers : 2.20 % Allowed : 12.71 % Favored : 85.10 % 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: -0.31 (0.11), residues: 6288 helix: 1.24 (0.13), residues: 1560 sheet: 1.32 (0.19), residues: 804 loop : -1.22 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 506 HIS 0.005 0.001 HIS b 432 PHE 0.014 0.002 PHE j 474 TYR 0.013 0.001 TYR e 350 ARG 0.004 0.000 ARG l 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 119 time to evaluate : 5.303 Fit side-chains REVERT: a 196 MET cc_start: 0.8986 (mmm) cc_final: 0.8767 (mmt) REVERT: a 264 MET cc_start: 0.8712 (tmm) cc_final: 0.8259 (tmm) REVERT: b 107 MET cc_start: 0.8041 (mmm) cc_final: 0.7748 (mmt) REVERT: c 264 MET cc_start: 0.8602 (tmm) cc_final: 0.8277 (tmm) REVERT: d 196 MET cc_start: 0.8972 (mmm) cc_final: 0.8751 (mmt) REVERT: d 264 MET cc_start: 0.8730 (tmm) cc_final: 0.8283 (tmm) REVERT: d 367 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7665 (m170) REVERT: e 107 MET cc_start: 0.8029 (mmm) cc_final: 0.7737 (mmt) REVERT: f 264 MET cc_start: 0.8602 (tmm) cc_final: 0.8270 (tmm) REVERT: g 413 MET cc_start: 0.8378 (mmm) cc_final: 0.8087 (mmt) REVERT: g 437 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: h 367 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7017 (m170) REVERT: h 500 GLN cc_start: 0.5923 (tm-30) cc_final: 0.5689 (tm-30) REVERT: i 367 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6750 (m170) REVERT: j 343 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: k 367 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6997 (m170) REVERT: k 500 GLN cc_start: 0.5899 (tm-30) cc_final: 0.5617 (tm-30) REVERT: l 264 MET cc_start: 0.7495 (tpp) cc_final: 0.7123 (tpp) REVERT: l 367 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6610 (m170) outliers start: 112 outliers final: 63 residues processed: 225 average time/residue: 0.5027 time to fit residues: 204.4324 Evaluate side-chains 183 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 113 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 367 HIS Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 437 MET Chi-restraints excluded: chain b residue 526 LEU Chi-restraints excluded: chain c residue 222 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 414 ILE Chi-restraints excluded: chain c residue 437 MET Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 217 VAL Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 367 HIS Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 414 ILE Chi-restraints excluded: chain e residue 526 LEU Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 414 ILE Chi-restraints excluded: chain f residue 506 TRP Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 180 THR Chi-restraints excluded: chain g residue 323 CYS Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS Chi-restraints excluded: chain h residue 323 CYS Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 323 CYS Chi-restraints excluded: chain i residue 367 HIS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 180 THR Chi-restraints excluded: chain j residue 323 CYS Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 239 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 323 CYS Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 441 SER Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 323 CYS Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 510 TRP Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 440 optimal weight: 30.0000 chunk 341 optimal weight: 3.9990 chunk 508 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 601 optimal weight: 20.0000 chunk 376 optimal weight: 2.9990 chunk 366 optimal weight: 40.0000 chunk 277 optimal weight: 0.0570 overall best weight: 3.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 432 HIS ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 432 HIS ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 HIS ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 432 HIS i 432 HIS i 522 GLN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48648 Z= 0.170 Angle : 0.517 9.001 66252 Z= 0.270 Chirality : 0.042 0.200 7644 Planarity : 0.005 0.089 8592 Dihedral : 4.529 22.675 6816 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.04 % Favored : 95.53 % Rotamer: Outliers : 1.61 % Allowed : 13.04 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.11), residues: 6288 helix: 1.46 (0.14), residues: 1560 sheet: 1.44 (0.19), residues: 804 loop : -1.13 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP f 506 HIS 0.007 0.001 HIS b 432 PHE 0.009 0.001 PHE j 474 TYR 0.010 0.001 TYR e 350 ARG 0.004 0.000 ARG l 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 121 time to evaluate : 5.405 Fit side-chains REVERT: a 196 MET cc_start: 0.8835 (mmm) cc_final: 0.8616 (mmt) REVERT: a 264 MET cc_start: 0.8691 (tmm) cc_final: 0.8360 (tmm) REVERT: d 196 MET cc_start: 0.8860 (mmm) cc_final: 0.8638 (mmt) REVERT: d 264 MET cc_start: 0.8687 (tmm) cc_final: 0.8377 (tmm) REVERT: e 264 MET cc_start: 0.8567 (tmm) cc_final: 0.8285 (tmm) REVERT: g 413 MET cc_start: 0.8344 (mmm) cc_final: 0.8079 (mmt) REVERT: g 437 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7646 (mmm) REVERT: g 451 MET cc_start: 0.7498 (mmp) cc_final: 0.6662 (mtt) REVERT: g 500 GLN cc_start: 0.6002 (tm-30) cc_final: 0.5764 (tm-30) REVERT: h 367 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.6637 (m170) REVERT: i 367 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6661 (m170) REVERT: j 451 MET cc_start: 0.7223 (mmp) cc_final: 0.6732 (mmm) REVERT: j 500 GLN cc_start: 0.5991 (tm-30) cc_final: 0.5750 (tm-30) REVERT: l 451 MET cc_start: 0.6846 (mmp) cc_final: 0.6619 (mmm) outliers start: 82 outliers final: 51 residues processed: 198 average time/residue: 0.5040 time to fit residues: 182.7357 Evaluate side-chains 168 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 279 ILE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain a residue 367 HIS Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 367 HIS Chi-restraints excluded: chain b residue 414 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 402 LEU Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 367 HIS Chi-restraints excluded: chain e residue 414 ILE Chi-restraints excluded: chain f residue 222 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 286 CYS Chi-restraints excluded: chain i residue 367 HIS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 239 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 510 TRP Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 359 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 116 optimal weight: 40.0000 chunk 382 optimal weight: 10.0000 chunk 409 optimal weight: 0.8980 chunk 297 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 472 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 GLN ** a 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 432 HIS ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 75 GLN ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 432 HIS ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 432 HIS h 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48648 Z= 0.167 Angle : 0.517 7.847 66252 Z= 0.268 Chirality : 0.042 0.169 7644 Planarity : 0.005 0.090 8592 Dihedral : 4.422 22.233 6816 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.96 % Favored : 95.64 % Rotamer: Outliers : 1.59 % Allowed : 13.12 % Favored : 85.29 % 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: -0.06 (0.11), residues: 6288 helix: 1.56 (0.14), residues: 1560 sheet: 1.47 (0.19), residues: 804 loop : -1.11 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP f 506 HIS 0.006 0.001 HIS g 432 PHE 0.009 0.001 PHE i 474 TYR 0.011 0.001 TYR b 350 ARG 0.003 0.000 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 123 time to evaluate : 5.289 Fit side-chains REVERT: a 196 MET cc_start: 0.8852 (mmm) cc_final: 0.8637 (mmt) REVERT: a 264 MET cc_start: 0.8632 (tmm) cc_final: 0.8412 (tmm) REVERT: d 196 MET cc_start: 0.8838 (mmm) cc_final: 0.8623 (mmt) REVERT: d 264 MET cc_start: 0.8646 (tmm) cc_final: 0.8364 (tmm) REVERT: d 343 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8491 (t80) REVERT: e 264 MET cc_start: 0.8566 (tmm) cc_final: 0.8327 (tmm) REVERT: g 367 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7010 (m170) REVERT: g 413 MET cc_start: 0.8311 (mmm) cc_final: 0.8083 (mmt) REVERT: g 437 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7657 (mmm) REVERT: h 367 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6758 (m170) REVERT: h 467 MET cc_start: 0.8378 (mmm) cc_final: 0.8022 (mmp) REVERT: j 343 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: j 451 MET cc_start: 0.7338 (mmp) cc_final: 0.6774 (mmm) REVERT: k 367 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7144 (m170) REVERT: l 367 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6708 (m170) REVERT: l 451 MET cc_start: 0.6831 (mmp) cc_final: 0.6600 (mmm) outliers start: 81 outliers final: 57 residues processed: 200 average time/residue: 0.5021 time to fit residues: 183.7398 Evaluate side-chains 180 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 279 ILE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain a residue 367 HIS Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 367 HIS Chi-restraints excluded: chain b residue 414 ILE Chi-restraints excluded: chain b residue 458 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 279 ILE Chi-restraints excluded: chain d residue 343 PHE Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 367 HIS Chi-restraints excluded: chain e residue 414 ILE Chi-restraints excluded: chain e residue 458 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 458 ILE Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 286 CYS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain i residue 526 LEU Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 510 TRP Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 9.9990 chunk 576 optimal weight: 3.9990 chunk 525 optimal weight: 3.9990 chunk 560 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 440 optimal weight: 9.9990 chunk 171 optimal weight: 50.0000 chunk 506 optimal weight: 5.9990 chunk 530 optimal weight: 20.0000 chunk 558 optimal weight: 20.0000 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 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 432 HIS ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 218 ASN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48648 Z= 0.222 Angle : 0.549 11.041 66252 Z= 0.285 Chirality : 0.043 0.221 7644 Planarity : 0.005 0.086 8592 Dihedral : 4.556 23.420 6816 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.71 % Favored : 94.83 % Rotamer: Outliers : 1.61 % Allowed : 13.14 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.11), residues: 6288 helix: 1.56 (0.14), residues: 1560 sheet: 1.48 (0.19), residues: 804 loop : -1.14 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP j 506 HIS 0.013 0.001 HIS i 432 PHE 0.011 0.001 PHE j 474 TYR 0.013 0.001 TYR b 350 ARG 0.004 0.000 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 116 time to evaluate : 4.799 Fit side-chains REVERT: a 196 MET cc_start: 0.8853 (mmm) cc_final: 0.8648 (mmt) REVERT: a 264 MET cc_start: 0.8701 (tmm) cc_final: 0.8349 (tmm) REVERT: d 196 MET cc_start: 0.8872 (mmm) cc_final: 0.8667 (mmt) REVERT: d 264 MET cc_start: 0.8711 (tmm) cc_final: 0.8309 (tmm) REVERT: e 264 MET cc_start: 0.8561 (tmm) cc_final: 0.8278 (tmm) REVERT: g 343 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: g 413 MET cc_start: 0.8377 (mmm) cc_final: 0.8131 (mmt) REVERT: g 437 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7713 (mmm) REVERT: g 451 MET cc_start: 0.7433 (mmp) cc_final: 0.7119 (mtt) REVERT: h 367 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7092 (m170) REVERT: h 467 MET cc_start: 0.8422 (mmm) cc_final: 0.8051 (mmp) REVERT: j 343 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: k 367 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7144 (m170) REVERT: l 367 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6720 (m170) outliers start: 82 outliers final: 62 residues processed: 192 average time/residue: 0.4757 time to fit residues: 168.1576 Evaluate side-chains 182 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain a residue 367 HIS Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 367 HIS Chi-restraints excluded: chain b residue 414 ILE Chi-restraints excluded: chain b residue 458 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 402 LEU Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 343 PHE Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain d residue 458 ILE Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 367 HIS Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 414 ILE Chi-restraints excluded: chain e residue 458 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 458 ILE Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 343 PHE Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS Chi-restraints excluded: chain h residue 343 PHE Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 286 CYS Chi-restraints excluded: chain i residue 441 SER Chi-restraints excluded: chain i residue 453 HIS Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 432 HIS Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 510 TRP Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 1.9990 chunk 592 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 411 optimal weight: 0.9990 chunk 621 optimal weight: 8.9990 chunk 572 optimal weight: 30.0000 chunk 495 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.7717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48648 Z= 0.173 Angle : 0.524 9.315 66252 Z= 0.272 Chirality : 0.042 0.214 7644 Planarity : 0.004 0.084 8592 Dihedral : 4.455 22.408 6816 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.96 % Favored : 95.63 % Rotamer: Outliers : 1.29 % Allowed : 13.49 % Favored : 85.22 % 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: -0.05 (0.11), residues: 6288 helix: 1.59 (0.14), residues: 1560 sheet: 1.52 (0.19), residues: 804 loop : -1.12 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP j 506 HIS 0.011 0.001 HIS j 432 PHE 0.015 0.001 PHE l 474 TYR 0.014 0.001 TYR d 368 ARG 0.004 0.000 ARG e 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 119 time to evaluate : 4.516 Fit side-chains REVERT: a 196 MET cc_start: 0.8848 (mmm) cc_final: 0.8644 (mmt) REVERT: a 264 MET cc_start: 0.8686 (tmm) cc_final: 0.8358 (tmm) REVERT: d 196 MET cc_start: 0.8832 (mmm) cc_final: 0.8627 (mmt) REVERT: d 264 MET cc_start: 0.8703 (tmm) cc_final: 0.8394 (tmm) REVERT: e 264 MET cc_start: 0.8559 (tmm) cc_final: 0.8299 (tmm) REVERT: g 367 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6873 (m170) REVERT: g 413 MET cc_start: 0.8365 (mmm) cc_final: 0.8124 (mmt) REVERT: g 437 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7641 (mmm) REVERT: g 451 MET cc_start: 0.7447 (mmp) cc_final: 0.7075 (mtt) REVERT: h 367 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.7059 (m170) REVERT: h 467 MET cc_start: 0.8381 (mmm) cc_final: 0.8006 (mmp) REVERT: i 451 MET cc_start: 0.6776 (mmp) cc_final: 0.6558 (mmm) REVERT: j 343 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: k 367 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7159 (m170) REVERT: l 367 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6778 (m170) outliers start: 66 outliers final: 58 residues processed: 180 average time/residue: 0.4281 time to fit residues: 140.8391 Evaluate side-chains 181 residues out of total 5124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 363 VAL Chi-restraints excluded: chain a residue 367 HIS Chi-restraints excluded: chain a residue 414 ILE Chi-restraints excluded: chain a residue 458 ILE Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 367 HIS Chi-restraints excluded: chain b residue 414 ILE Chi-restraints excluded: chain b residue 458 ILE Chi-restraints excluded: chain c residue 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 402 LEU Chi-restraints excluded: chain c residue 506 TRP Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain d residue 458 ILE Chi-restraints excluded: chain e residue 343 PHE Chi-restraints excluded: chain e residue 367 HIS Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 414 ILE Chi-restraints excluded: chain e residue 458 ILE Chi-restraints excluded: chain f residue 343 PHE Chi-restraints excluded: chain f residue 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 458 ILE Chi-restraints excluded: chain g residue 124 GLU Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS Chi-restraints excluded: chain g residue 437 MET Chi-restraints excluded: chain g residue 510 TRP Chi-restraints excluded: chain h residue 53 LEU Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS Chi-restraints excluded: chain h residue 343 PHE Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 510 TRP Chi-restraints excluded: chain h residue 526 LEU Chi-restraints excluded: chain i residue 156 THR Chi-restraints excluded: chain i residue 510 TRP Chi-restraints excluded: chain i residue 526 LEU Chi-restraints excluded: chain j residue 156 THR Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain j residue 343 PHE Chi-restraints excluded: chain j residue 367 HIS Chi-restraints excluded: chain j residue 432 HIS Chi-restraints excluded: chain j residue 510 TRP Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 156 THR Chi-restraints excluded: chain k residue 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 343 PHE Chi-restraints excluded: chain k residue 367 HIS Chi-restraints excluded: chain k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 156 THR Chi-restraints excluded: chain l residue 180 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 510 TRP Chi-restraints excluded: chain l residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 20.0000 chunk 527 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 456 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 495 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 509 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 432 HIS ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.043745 restraints weight = 251740.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044785 restraints weight = 140238.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045486 restraints weight = 92836.020| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48648 Z= 0.255 Angle : 0.565 9.623 66252 Z= 0.295 Chirality : 0.043 0.239 7644 Planarity : 0.005 0.082 8592 Dihedral : 4.671 24.073 6816 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.79 % Favored : 94.67 % Rotamer: Outliers : 1.43 % Allowed : 13.45 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.11), residues: 6288 helix: 1.54 (0.14), residues: 1560 sheet: 1.45 (0.19), residues: 804 loop : -1.19 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP j 506 HIS 0.009 0.001 HIS j 429 PHE 0.019 0.002 PHE g 474 TYR 0.014 0.001 TYR b 350 ARG 0.005 0.000 ARG e 80 =============================================================================== Job complete usr+sys time: 6215.42 seconds wall clock time: 120 minutes 3.11 seconds (7203.11 seconds total)