Starting phenix.real_space_refine on Mon Sep 23 13:02:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/09_2024/8jaj_36127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/09_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_36127/09_2024/8jaj_36127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/09_2024/8jaj_36127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/09_2024/8jaj_36127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/09_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.22, per 1000 atoms: 0.21 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: 8.52 Conformation dependent library (CDL) restraints added in 4.8 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: 4.81 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: 14.47 Time building geometry restraints manager: 10.22 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.390 Check model and map are aligned: 0.280 Set scattering table: 0.320 Process input model: 68.350 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.120 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.900 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 4.058 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: 0.4580 time to fit residues: 423.3670 Evaluate side-chains 186 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.056 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 4.067 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: 0.4438 time to fit residues: 177.8437 Evaluate side-chains 160 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 4.098 ------------------------------------------------------------------------------- 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: 20.0000 chunk 175 optimal weight: 10.0000 chunk 471 optimal weight: 20.0000 chunk 385 optimal weight: 30.0000 chunk 156 optimal weight: 20.0000 chunk 567 optimal weight: 6.9990 chunk 613 optimal weight: 7.9990 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: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 522 GLN b 75 GLN ** b 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 522 GLN ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 522 GLN ** 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 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 522 GLN g 432 HIS ** h 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 429 HIS h 432 HIS h 522 GLN ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6515 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= 0.456 Angle : 0.730 7.991 66252 Z= 0.387 Chirality : 0.047 0.200 7644 Planarity : 0.006 0.085 8592 Dihedral : 5.423 27.271 6816 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.20 % Favored : 95.45 % Rotamer: Outliers : 1.75 % Allowed : 10.27 % Favored : 87.98 % 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: -0.33 (0.10), residues: 6288 helix: 0.99 (0.13), residues: 1572 sheet: 1.73 (0.18), residues: 804 loop : -1.23 (0.09), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 510 HIS 0.007 0.001 HIS h 432 PHE 0.023 0.003 PHE l 474 TYR 0.023 0.002 TYR h 350 ARG 0.006 0.001 ARG l 253 *********************** 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 230 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 141 time to evaluate : 4.143 Fit side-chains REVERT: a 264 MET cc_start: 0.8566 (tmm) cc_final: 0.7927 (tmm) REVERT: c 264 MET cc_start: 0.8606 (tmm) cc_final: 0.8302 (tmm) REVERT: d 264 MET cc_start: 0.8664 (tmm) cc_final: 0.8141 (tmm) REVERT: f 264 MET cc_start: 0.8605 (tmm) cc_final: 0.8294 (tmm) REVERT: g 413 MET cc_start: 0.8446 (mmm) cc_final: 0.8084 (mmt) REVERT: h 107 MET cc_start: 0.7222 (mtt) cc_final: 0.6986 (mtp) REVERT: h 264 MET cc_start: 0.7719 (tpp) cc_final: 0.7458 (tpp) REVERT: h 367 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.7036 (m170) REVERT: i 264 MET cc_start: 0.7652 (tpp) cc_final: 0.7444 (tpp) REVERT: j 343 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (m-10) REVERT: j 413 MET cc_start: 0.8477 (mmm) cc_final: 0.8250 (mmt) REVERT: k 367 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7000 (m170) REVERT: k 432 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7121 (t70) REVERT: l 367 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6615 (m170) outliers start: 89 outliers final: 46 residues processed: 219 average time/residue: 0.4096 time to fit residues: 162.9511 Evaluate side-chains 162 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 343 PHE Chi-restraints excluded: chain a residue 437 MET 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 343 PHE Chi-restraints excluded: chain c residue 363 VAL Chi-restraints excluded: chain d residue 343 PHE Chi-restraints excluded: chain d residue 437 MET Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE 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 h residue 14 SER 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 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 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 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 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: 10.0000 chunk 294 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 381 optimal weight: 0.5980 chunk 569 optimal weight: 7.9990 chunk 603 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 539 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- 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 ** 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 429 HIS h 432 HIS j 429 HIS j 522 GLN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS l 522 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48648 Z= 0.215 Angle : 0.548 8.397 66252 Z= 0.289 Chirality : 0.043 0.154 7644 Planarity : 0.005 0.089 8592 Dihedral : 4.829 23.261 6816 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.29 % Favored : 95.42 % Rotamer: Outliers : 1.47 % Allowed : 12.06 % Favored : 86.47 % 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: -0.19 (0.10), residues: 6288 helix: 1.23 (0.13), residues: 1572 sheet: 1.67 (0.19), residues: 804 loop : -1.16 (0.09), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP i 506 HIS 0.004 0.001 HIS h 432 PHE 0.012 0.001 PHE l 474 TYR 0.010 0.001 TYR i 350 ARG 0.005 0.000 ARG l 253 *********************** 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 202 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 127 time to evaluate : 4.112 Fit side-chains REVERT: a 196 MET cc_start: 0.8879 (mmm) cc_final: 0.8599 (mmt) REVERT: a 264 MET cc_start: 0.8556 (tmm) cc_final: 0.8025 (tmm) REVERT: c 264 MET cc_start: 0.8522 (tmm) cc_final: 0.8159 (tmm) REVERT: d 196 MET cc_start: 0.8897 (mmm) cc_final: 0.8634 (mmt) REVERT: d 264 MET cc_start: 0.8624 (tmm) cc_final: 0.8202 (tmm) REVERT: e 196 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (mmm) REVERT: f 264 MET cc_start: 0.8517 (tmm) cc_final: 0.8151 (tmm) REVERT: g 367 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6924 (m170) REVERT: g 413 MET cc_start: 0.8398 (mmm) cc_final: 0.8078 (mmt) REVERT: h 526 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8573 (mt) REVERT: i 367 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6717 (m170) REVERT: k 432 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6354 (t70) REVERT: k 526 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8636 (tp) outliers start: 75 outliers final: 37 residues processed: 193 average time/residue: 0.4100 time to fit residues: 145.0007 Evaluate side-chains 165 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 217 VAL Chi-restraints excluded: chain a residue 279 ILE Chi-restraints excluded: chain b 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 363 VAL Chi-restraints excluded: chain d residue 217 VAL Chi-restraints excluded: chain d residue 279 ILE Chi-restraints excluded: chain e residue 196 MET Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE 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 14 SER Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 323 CYS 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 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 239 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 156 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 432 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 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: 8.9990 chunk 8 optimal weight: 20.0000 chunk 449 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 514 optimal weight: 7.9990 chunk 416 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 541 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 GLN ** a 453 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** d 75 GLN ** d 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 171 GLN ** 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 h 500 GLN i 75 GLN ** i 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 432 HIS j 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 48648 Z= 0.301 Angle : 0.602 8.251 66252 Z= 0.319 Chirality : 0.044 0.155 7644 Planarity : 0.005 0.090 8592 Dihedral : 5.009 24.719 6816 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.91 % Favored : 94.64 % Rotamer: Outliers : 2.04 % Allowed : 12.33 % Favored : 85.63 % 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: -0.28 (0.11), residues: 6288 helix: 1.18 (0.13), residues: 1560 sheet: 1.47 (0.19), residues: 804 loop : -1.20 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 506 HIS 0.004 0.001 HIS j 367 PHE 0.017 0.002 PHE j 474 TYR 0.018 0.001 TYR f 350 ARG 0.004 0.000 ARG e 80 *********************** 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 225 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 121 time to evaluate : 4.110 Fit side-chains REVERT: a 196 MET cc_start: 0.8990 (mmm) cc_final: 0.8770 (mmt) REVERT: a 264 MET cc_start: 0.8630 (tmm) cc_final: 0.8145 (tmm) REVERT: a 367 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7665 (m170) REVERT: c 264 MET cc_start: 0.8569 (tmm) cc_final: 0.8198 (tmm) REVERT: d 196 MET cc_start: 0.8953 (mmm) cc_final: 0.8747 (mmt) REVERT: d 264 MET cc_start: 0.8695 (tmm) cc_final: 0.8262 (tmm) REVERT: d 367 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7643 (m170) REVERT: f 264 MET cc_start: 0.8577 (tmm) cc_final: 0.8203 (tmm) REVERT: g 413 MET cc_start: 0.8466 (mmm) cc_final: 0.8167 (mmt) REVERT: g 467 MET cc_start: 0.8566 (mmm) cc_final: 0.8279 (mmm) REVERT: h 367 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7068 (m170) REVERT: h 500 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.5185 (tm-30) REVERT: i 367 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6645 (m170) REVERT: i 526 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8461 (mt) REVERT: k 367 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6975 (m170) REVERT: k 432 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6935 (t70) REVERT: k 437 MET cc_start: 0.8698 (mmp) cc_final: 0.8413 (mmp) REVERT: k 500 GLN cc_start: 0.5263 (tm-30) cc_final: 0.4988 (tm-30) REVERT: k 526 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8647 (tp) REVERT: l 367 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6632 (m170) outliers start: 104 outliers final: 50 residues processed: 217 average time/residue: 0.4027 time to fit residues: 160.1566 Evaluate side-chains 176 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 116 time to evaluate : 4.068 ------------------------------------------------------------------------------- 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 414 ILE 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 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 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 510 TRP Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 367 HIS Chi-restraints excluded: chain h residue 441 SER Chi-restraints excluded: chain h residue 500 GLN 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 367 HIS 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 180 THR Chi-restraints excluded: chain j residue 239 THR Chi-restraints excluded: chain j residue 323 CYS 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 180 THR 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 k residue 510 TRP Chi-restraints excluded: chain k residue 526 LEU Chi-restraints excluded: chain l residue 125 ILE Chi-restraints excluded: chain l residue 156 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 9.9990 chunk 543 optimal weight: 30.0000 chunk 119 optimal weight: 0.1980 chunk 354 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 603 optimal weight: 20.0000 chunk 501 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 overall best weight: 6.6388 ------------------------------------------------------------------------------- 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** ** 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 i 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 48648 Z= 0.236 Angle : 0.555 6.532 66252 Z= 0.292 Chirality : 0.043 0.171 7644 Planarity : 0.005 0.090 8592 Dihedral : 4.808 23.485 6816 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.29 % Favored : 95.20 % Rotamer: Outliers : 1.92 % Allowed : 12.76 % Favored : 85.31 % 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: -0.23 (0.11), residues: 6288 helix: 1.29 (0.13), residues: 1560 sheet: 1.42 (0.19), residues: 804 loop : -1.17 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP h 506 HIS 0.006 0.001 HIS b 432 PHE 0.012 0.002 PHE l 474 TYR 0.012 0.001 TYR b 350 ARG 0.004 0.000 ARG e 80 *********************** 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 222 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 124 time to evaluate : 4.117 Fit side-chains REVERT: a 196 MET cc_start: 0.8921 (mmm) cc_final: 0.8706 (mmt) REVERT: a 264 MET cc_start: 0.8636 (tmm) cc_final: 0.8190 (tmm) REVERT: b 107 MET cc_start: 0.8140 (mmm) cc_final: 0.7910 (mmt) REVERT: c 264 MET cc_start: 0.8594 (tmm) cc_final: 0.8253 (tmm) REVERT: d 196 MET cc_start: 0.8915 (mmm) cc_final: 0.8707 (mmt) REVERT: d 264 MET cc_start: 0.8708 (tmm) cc_final: 0.8266 (tmm) REVERT: d 367 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7727 (m170) REVERT: e 107 MET cc_start: 0.8133 (mmm) cc_final: 0.7908 (mmt) REVERT: e 196 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: f 264 MET cc_start: 0.8591 (tmm) cc_final: 0.8245 (tmm) REVERT: g 413 MET cc_start: 0.8403 (mmm) cc_final: 0.8116 (mmt) REVERT: h 500 GLN cc_start: 0.5679 (tm-30) cc_final: 0.5049 (tm-30) REVERT: i 367 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6701 (m170) REVERT: j 451 MET cc_start: 0.7594 (mmp) cc_final: 0.6847 (mtt) REVERT: k 500 GLN cc_start: 0.5388 (tm-30) cc_final: 0.5172 (tm-30) outliers start: 98 outliers final: 60 residues processed: 217 average time/residue: 0.4047 time to fit residues: 159.8031 Evaluate side-chains 180 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 117 time to evaluate : 4.099 ------------------------------------------------------------------------------- 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 a residue 402 LEU 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 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 506 TRP Chi-restraints excluded: chain d residue 217 VAL Chi-restraints excluded: chain d residue 222 ILE Chi-restraints excluded: chain d residue 363 VAL Chi-restraints excluded: chain d residue 367 HIS Chi-restraints excluded: chain e residue 196 MET Chi-restraints excluded: chain e residue 334 ASP Chi-restraints excluded: chain e residue 343 PHE 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 510 TRP Chi-restraints excluded: chain h residue 180 THR Chi-restraints excluded: chain h residue 286 CYS 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 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 173 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 173 THR Chi-restraints excluded: chain k residue 180 THR Chi-restraints excluded: chain k residue 286 CYS Chi-restraints excluded: chain k residue 323 CYS 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 180 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 510 TRP 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: 7.9990 chunk 343 optimal weight: 20.0000 chunk 440 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 508 optimal weight: 0.4980 chunk 337 optimal weight: 8.9990 chunk 601 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 366 optimal weight: 40.0000 chunk 277 optimal weight: 6.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- 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** ** 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** g 218 ASN h 432 HIS i 432 HIS i 522 GLN ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 429 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48648 Z= 0.230 Angle : 0.549 8.561 66252 Z= 0.288 Chirality : 0.043 0.163 7644 Planarity : 0.005 0.089 8592 Dihedral : 4.730 23.306 6816 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.64 % Favored : 94.82 % Rotamer: Outliers : 2.10 % Allowed : 12.55 % 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: -0.23 (0.11), residues: 6288 helix: 1.34 (0.13), residues: 1560 sheet: 1.40 (0.19), residues: 804 loop : -1.19 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 506 HIS 0.008 0.001 HIS a 367 PHE 0.012 0.001 PHE j 474 TYR 0.015 0.001 TYR a 368 ARG 0.004 0.000 ARG e 80 *********************** 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 231 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 124 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 196 MET cc_start: 0.8974 (mmm) cc_final: 0.8756 (mmt) REVERT: a 264 MET cc_start: 0.8630 (tmm) cc_final: 0.8198 (tmm) REVERT: b 107 MET cc_start: 0.8177 (mmm) cc_final: 0.7960 (mmt) REVERT: c 264 MET cc_start: 0.8586 (tmm) cc_final: 0.8256 (tmm) REVERT: d 196 MET cc_start: 0.8953 (mmm) cc_final: 0.8738 (mmt) REVERT: d 264 MET cc_start: 0.8682 (tmm) cc_final: 0.8246 (tmm) REVERT: d 367 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7610 (m170) REVERT: e 107 MET cc_start: 0.8152 (mmm) cc_final: 0.7929 (mmt) REVERT: f 264 MET cc_start: 0.8587 (tmm) cc_final: 0.8250 (tmm) REVERT: g 413 MET cc_start: 0.8376 (mmm) cc_final: 0.8114 (mmt) REVERT: h 367 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.6804 (m170) REVERT: h 500 GLN cc_start: 0.5772 (tm-30) cc_final: 0.5493 (tm-30) REVERT: i 367 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6553 (m170) REVERT: j 451 MET cc_start: 0.7614 (mmp) cc_final: 0.6934 (mtt) REVERT: k 367 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6964 (m170) REVERT: k 500 GLN cc_start: 0.5794 (tm-30) cc_final: 0.5456 (tm-30) REVERT: l 367 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6732 (m170) outliers start: 107 outliers final: 63 residues processed: 225 average time/residue: 0.4180 time to fit residues: 169.6791 Evaluate side-chains 186 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 118 time to evaluate : 4.110 ------------------------------------------------------------------------------- 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 367 HIS Chi-restraints excluded: chain b residue 414 ILE 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 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 217 VAL Chi-restraints excluded: chain d residue 222 ILE 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 367 HIS 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 437 MET 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 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 125 ILE 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 173 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 173 THR Chi-restraints excluded: chain k residue 180 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 116 optimal weight: 0.1980 chunk 382 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 472 optimal weight: 2.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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** ** 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: 0.8367 moved from start: 0.7544 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= 0.172 Angle : 0.517 7.634 66252 Z= 0.270 Chirality : 0.042 0.177 7644 Planarity : 0.005 0.089 8592 Dihedral : 4.493 21.993 6816 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.82 % Favored : 95.75 % Rotamer: Outliers : 1.59 % Allowed : 12.88 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.11), residues: 6288 helix: 1.50 (0.14), residues: 1560 sheet: 1.47 (0.19), residues: 804 loop : -1.12 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP f 506 HIS 0.006 0.001 HIS b 432 PHE 0.013 0.001 PHE l 474 TYR 0.010 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 fitting. rotamer outliers: 81 poor density : 123 time to evaluate : 4.155 Fit side-chains REVERT: a 196 MET cc_start: 0.8865 (mmm) cc_final: 0.8650 (mmt) REVERT: a 264 MET cc_start: 0.8620 (tmm) cc_final: 0.8224 (tmm) REVERT: b 107 MET cc_start: 0.8163 (mmm) cc_final: 0.7951 (mmt) REVERT: d 196 MET cc_start: 0.8865 (mmm) cc_final: 0.8653 (mmt) REVERT: d 264 MET cc_start: 0.8677 (tmm) cc_final: 0.8282 (tmm) REVERT: e 107 MET cc_start: 0.8141 (mmm) cc_final: 0.7939 (mmt) REVERT: e 196 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: g 413 MET cc_start: 0.8362 (mmm) cc_final: 0.8108 (mmt) REVERT: g 451 MET cc_start: 0.7328 (mmp) cc_final: 0.6878 (mtt) REVERT: g 500 GLN cc_start: 0.5969 (tm-30) cc_final: 0.5737 (tm-30) REVERT: h 367 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.7015 (m170) REVERT: h 467 MET cc_start: 0.8363 (mmm) cc_final: 0.8039 (mmp) REVERT: h 500 GLN cc_start: 0.5762 (tm-30) cc_final: 0.5502 (tm-30) REVERT: i 367 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6386 (m170) REVERT: k 367 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6963 (m170) REVERT: k 467 MET cc_start: 0.8395 (mmm) cc_final: 0.8036 (mmp) REVERT: l 367 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6803 (m170) outliers start: 81 outliers final: 54 residues processed: 195 average time/residue: 0.4163 time to fit residues: 148.0231 Evaluate side-chains 175 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 4.085 ------------------------------------------------------------------------------- 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 402 LEU 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 c residue 363 VAL Chi-restraints excluded: chain c residue 367 HIS Chi-restraints excluded: chain c residue 437 MET 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 402 LEU Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain e residue 196 MET 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 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 437 MET Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS 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 125 ILE 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 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 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 367 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 180 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 453 HIS Chi-restraints excluded: chain l residue 510 TRP 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: 2.9990 chunk 525 optimal weight: 6.9990 chunk 560 optimal weight: 0.0870 chunk 337 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 440 optimal weight: 30.0000 chunk 171 optimal weight: 50.0000 chunk 506 optimal weight: 9.9990 chunk 530 optimal weight: 20.0000 chunk 558 optimal weight: 30.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- 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 426 ASN ** 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 i 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48648 Z= 0.212 Angle : 0.539 8.083 66252 Z= 0.281 Chirality : 0.042 0.201 7644 Planarity : 0.005 0.088 8592 Dihedral : 4.555 22.938 6816 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.61 % Favored : 94.90 % Rotamer: Outliers : 1.59 % Allowed : 12.96 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 6288 helix: 1.53 (0.14), residues: 1560 sheet: 1.49 (0.19), residues: 804 loop : -1.15 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP j 506 HIS 0.008 0.001 HIS i 432 PHE 0.015 0.001 PHE g 474 TYR 0.019 0.001 TYR d 368 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 202 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 121 time to evaluate : 4.136 Fit side-chains REVERT: a 196 MET cc_start: 0.8857 (mmm) cc_final: 0.8650 (mmt) REVERT: a 264 MET cc_start: 0.8621 (tmm) cc_final: 0.8208 (tmm) REVERT: d 196 MET cc_start: 0.8834 (mmm) cc_final: 0.8633 (mmt) REVERT: d 264 MET cc_start: 0.8688 (tmm) cc_final: 0.8283 (tmm) REVERT: g 413 MET cc_start: 0.8379 (mmm) cc_final: 0.8132 (mmt) REVERT: g 451 MET cc_start: 0.7476 (mmp) cc_final: 0.6977 (mtt) REVERT: h 367 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6970 (m170) REVERT: h 467 MET cc_start: 0.8402 (mmm) cc_final: 0.8045 (mmp) REVERT: h 500 GLN cc_start: 0.5812 (tm-30) cc_final: 0.5526 (tm-30) REVERT: i 367 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6520 (m170) REVERT: j 451 MET cc_start: 0.7484 (mmp) cc_final: 0.6750 (mtt) REVERT: k 367 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6990 (m170) REVERT: k 467 MET cc_start: 0.8407 (mmm) cc_final: 0.8047 (mmp) REVERT: l 367 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6699 (m170) outliers start: 81 outliers final: 64 residues processed: 195 average time/residue: 0.4514 time to fit residues: 160.8225 Evaluate side-chains 187 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 119 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 a residue 402 LEU 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 437 MET 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 402 LEU Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain e residue 334 ASP 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 402 LEU Chi-restraints excluded: chain f residue 437 MET Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS 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 125 ILE Chi-restraints excluded: chain i residue 156 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 453 HIS 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 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 441 SER Chi-restraints excluded: chain k residue 510 TRP 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 453 HIS Chi-restraints excluded: chain l residue 510 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 8.9990 chunk 592 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 411 optimal weight: 0.9990 chunk 621 optimal weight: 0.3980 chunk 572 optimal weight: 30.0000 chunk 495 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 382 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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** ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.7660 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= 0.171 Angle : 0.521 8.198 66252 Z= 0.270 Chirality : 0.042 0.180 7644 Planarity : 0.004 0.088 8592 Dihedral : 4.428 21.742 6816 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.69 % Favored : 95.90 % Rotamer: Outliers : 1.25 % Allowed : 13.35 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.11), residues: 6288 helix: 1.58 (0.14), residues: 1560 sheet: 1.52 (0.19), residues: 804 loop : -1.10 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP j 506 HIS 0.007 0.001 HIS i 432 PHE 0.014 0.001 PHE g 474 TYR 0.010 0.001 TYR e 350 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 187 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 123 time to evaluate : 4.082 Fit side-chains REVERT: a 196 MET cc_start: 0.8841 (mmm) cc_final: 0.8634 (mmt) REVERT: a 264 MET cc_start: 0.8689 (tmm) cc_final: 0.8256 (tmm) REVERT: d 196 MET cc_start: 0.8823 (mmm) cc_final: 0.8620 (mmt) REVERT: d 264 MET cc_start: 0.8684 (tmm) cc_final: 0.8375 (tmm) REVERT: e 196 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: g 367 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6782 (m170) REVERT: g 413 MET cc_start: 0.8348 (mmm) cc_final: 0.8112 (mmt) REVERT: g 451 MET cc_start: 0.7503 (mmp) cc_final: 0.6820 (mtt) REVERT: h 367 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7013 (m170) REVERT: h 467 MET cc_start: 0.8356 (mmm) cc_final: 0.7992 (mmp) REVERT: h 500 GLN cc_start: 0.5856 (tm-30) cc_final: 0.5597 (tm-30) REVERT: i 367 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6325 (m170) REVERT: j 367 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6988 (m170) REVERT: k 367 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7048 (m170) REVERT: k 467 MET cc_start: 0.8402 (mmm) cc_final: 0.8006 (mmp) REVERT: l 367 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6778 (m170) REVERT: l 451 MET cc_start: 0.7041 (mmp) cc_final: 0.6836 (mmm) outliers start: 64 outliers final: 51 residues processed: 180 average time/residue: 0.4092 time to fit residues: 134.4594 Evaluate side-chains 179 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 4.025 ------------------------------------------------------------------------------- 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 402 LEU 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 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 402 LEU Chi-restraints excluded: chain d residue 414 ILE Chi-restraints excluded: chain e residue 196 MET 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 363 VAL Chi-restraints excluded: chain f residue 367 HIS Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 437 MET Chi-restraints excluded: chain g residue 156 THR Chi-restraints excluded: chain g residue 367 HIS 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 510 TRP Chi-restraints excluded: chain i residue 125 ILE Chi-restraints excluded: chain i residue 156 THR 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 173 THR 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 367 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 180 THR Chi-restraints excluded: chain l residue 239 THR Chi-restraints excluded: chain l residue 367 HIS Chi-restraints excluded: chain l residue 453 HIS Chi-restraints excluded: chain l residue 510 TRP 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: 10.0000 chunk 151 optimal weight: 6.9990 chunk 456 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 495 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 509 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.052065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044427 restraints weight = 250442.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045494 restraints weight = 139204.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046205 restraints weight = 91955.931| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.7743 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= 0.207 Angle : 0.540 7.713 66252 Z= 0.280 Chirality : 0.042 0.179 7644 Planarity : 0.005 0.083 8592 Dihedral : 4.503 22.832 6816 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.36 % Favored : 95.17 % Rotamer: Outliers : 1.37 % Allowed : 13.43 % Favored : 85.20 % 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: 1.58 (0.14), residues: 1560 sheet: 1.53 (0.19), residues: 804 loop : -1.13 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP j 506 HIS 0.008 0.001 HIS i 432 PHE 0.016 0.001 PHE g 474 TYR 0.012 0.001 TYR b 350 ARG 0.004 0.000 ARG e 80 =============================================================================== Job complete usr+sys time: 5345.20 seconds wall clock time: 96 minutes 17.37 seconds (5777.37 seconds total)