Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 18:34:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/07_2023/8jaj_36127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/07_2023/8jaj_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_36127/07_2023/8jaj_36127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/07_2023/8jaj_36127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/07_2023/8jaj_36127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jaj_36127/07_2023/8jaj_36127.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "a TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 456": "OD1" <-> "OD2" Residue "b TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 456": "OD1" <-> "OD2" Residue "c TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 456": "OD1" <-> "OD2" Residue "d TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 456": "OD1" <-> "OD2" Residue "e TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 456": "OD1" <-> "OD2" Residue "f TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 456": "OD1" <-> "OD2" Residue "g TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 456": "OD1" <-> "OD2" Residue "h TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 456": "OD1" <-> "OD2" Residue "i TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 456": "OD1" <-> "OD2" Residue "j TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 456": "OD1" <-> "OD2" Residue "k TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 456": "OD1" <-> "OD2" Residue "l TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 456": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 47664 Number of models: 1 Model: "" Number of chains: 12 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 Chain: "b" 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 Chain: "c" 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 Chain: "d" 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 Chain: "e" 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 Chain: "f" 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 Chain: "g" 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 Chain: "h" 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 Chain: "i" 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 Chain: "j" 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 Chain: "k" 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 Chain: "l" 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 Time building chain proxies: 22.93, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 18.77 Conformation dependent library (CDL) restraints added in 7.2 seconds 12576 Ramachandran restraints generated. 6288 Oldfield, 0 Emsley, 6288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11640 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 78 sheets defined 26.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 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: 17.52 Time building geometry restraints manager: 20.03 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: 100.40 - 107.12: 1533 107.12 - 113.84: 27528 113.84 - 120.57: 18286 120.57 - 127.29: 18435 127.29 - 134.01: 470 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 2.520 nonbonded pdb=" ND2 ASN c 426 " pdb=" O ALA h 23 " model vdw 2.073 2.520 nonbonded pdb=" ND2 ASN e 426 " pdb=" O ALA j 23 " model vdw 2.110 2.520 nonbonded pdb=" ND2 ASN d 426 " pdb=" O ALA i 23 " model vdw 2.127 2.520 nonbonded pdb=" ND2 ASN f 426 " pdb=" O ALA k 23 " model vdw 2.128 2.520 ... (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 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: 1.910 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: 0.050 Extract box with map and model: 14.080 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 111.490 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.320 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.770 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 5.705 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: 0.5706 time to fit residues: 523.2386 Evaluate side-chains 186 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 5.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4890 ------------------------------------------------------------------------------- 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: 2.9990 chunk 262 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 566 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 75 GLN g 162 ASN g 500 GLN i 500 GLN j 162 ASN j 500 GLN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 48648 Z= 0.348 Angle : 0.755 12.624 66252 Z= 0.395 Chirality : 0.048 0.189 7644 Planarity : 0.006 0.080 8592 Dihedral : 5.387 24.772 6816 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.12 % Favored : 94.53 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 6288 helix: 1.06 (0.13), residues: 1548 sheet: 1.68 (0.17), residues: 912 loop : -1.21 (0.09), residues: 3828 *********************** 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 239 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 169 time to evaluate : 5.938 Fit side-chains outliers start: 70 outliers final: 34 residues processed: 226 average time/residue: 0.5421 time to fit residues: 216.0644 Evaluate side-chains 157 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 5.520 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4097 time to fit residues: 33.7587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 471 optimal weight: 7.9990 chunk 385 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 613 optimal weight: 20.0000 chunk 505 optimal weight: 20.0000 chunk 562 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 500 GLN ** 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: 0.8303 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 48648 Z= 0.256 Angle : 0.562 8.596 66252 Z= 0.294 Chirality : 0.043 0.155 7644 Planarity : 0.005 0.088 8592 Dihedral : 4.732 23.868 6816 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.37 % Favored : 96.36 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 6288 helix: 1.37 (0.13), residues: 1560 sheet: 1.65 (0.17), residues: 912 loop : -1.12 (0.10), residues: 3816 *********************** 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 181 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 5.641 Fit side-chains outliers start: 46 outliers final: 18 residues processed: 175 average time/residue: 0.5268 time to fit residues: 166.8386 Evaluate side-chains 143 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 5.303 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4470 time to fit residues: 21.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 0.9990 chunk 426 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 381 optimal weight: 0.5980 chunk 569 optimal weight: 5.9990 chunk 603 optimal weight: 20.0000 chunk 297 optimal weight: 0.0000 chunk 539 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 2.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 432 HIS h 500 GLN i 432 HIS j 500 GLN ** 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: 0.8262 moved from start: 0.6199 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= 0.143 Angle : 0.487 7.612 66252 Z= 0.252 Chirality : 0.041 0.152 7644 Planarity : 0.005 0.087 8592 Dihedral : 4.330 22.119 6816 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.59 % Favored : 96.15 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 6288 helix: 1.63 (0.13), residues: 1548 sheet: 1.67 (0.17), residues: 912 loop : -1.03 (0.10), residues: 3828 *********************** 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 157 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 5.257 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 154 average time/residue: 0.5234 time to fit residues: 146.1472 Evaluate side-chains 133 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 5.302 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4300 time to fit residues: 13.5266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 8.9990 chunk 342 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 449 optimal weight: 9.9990 chunk 248 optimal weight: 30.0000 chunk 514 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 541 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 GLN ** a 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 GLN b 162 ASN ** b 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 ASN ** c 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 75 GLN e 162 ASN ** e 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 ASN ** f 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 432 HIS ** h 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN i 432 HIS j 432 HIS k 75 GLN ** k 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 500 GLN ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 48648 Z= 0.290 Angle : 0.584 6.784 66252 Z= 0.308 Chirality : 0.043 0.153 7644 Planarity : 0.005 0.086 8592 Dihedral : 4.872 25.055 6816 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.99 % Favored : 94.67 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 6288 helix: 1.36 (0.14), residues: 1572 sheet: 1.75 (0.19), residues: 804 loop : -1.17 (0.10), residues: 3912 *********************** 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 179 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 122 time to evaluate : 5.391 Fit side-chains outliers start: 57 outliers final: 12 residues processed: 175 average time/residue: 0.5148 time to fit residues: 165.5552 Evaluate side-chains 127 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4392 time to fit residues: 17.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 6.9990 chunk 543 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 0.0670 chunk 501 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 overall best weight: 4.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 75 GLN a 162 ASN b 432 HIS c 432 HIS d 75 GLN d 162 ASN e 432 HIS f 432 HIS g 218 ASN g 432 HIS i 432 HIS j 432 HIS l 432 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.7001 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= 0.173 Angle : 0.508 6.951 66252 Z= 0.265 Chirality : 0.042 0.221 7644 Planarity : 0.005 0.085 8592 Dihedral : 4.537 22.266 6816 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.64 % Favored : 95.98 % Rotamer Outliers : 1.18 % 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: -0.01 (0.11), residues: 6288 helix: 1.50 (0.14), residues: 1572 sheet: 1.48 (0.17), residues: 912 loop : -1.11 (0.10), residues: 3804 *********************** 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 184 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 124 time to evaluate : 6.364 Fit side-chains outliers start: 60 outliers final: 18 residues processed: 180 average time/residue: 0.4981 time to fit residues: 164.5092 Evaluate side-chains 136 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4263 time to fit residues: 21.2549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 343 optimal weight: 20.0000 chunk 440 optimal weight: 30.0000 chunk 341 optimal weight: 7.9990 chunk 508 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 601 optimal weight: 20.0000 chunk 376 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 277 optimal weight: 0.0020 overall best weight: 4.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 432 HIS ** c 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 432 HIS e 432 HIS ** f 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 432 HIS g 432 HIS i 432 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 48648 Z= 0.180 Angle : 0.509 7.085 66252 Z= 0.264 Chirality : 0.042 0.175 7644 Planarity : 0.005 0.085 8592 Dihedral : 4.424 22.063 6816 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.02 % Favored : 95.67 % Rotamer Outliers : 0.47 % 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: 0.02 (0.11), residues: 6288 helix: 1.59 (0.14), residues: 1572 sheet: 1.73 (0.19), residues: 804 loop : -1.11 (0.10), residues: 3912 *********************** 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 142 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 5.706 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 139 average time/residue: 0.5174 time to fit residues: 132.2817 Evaluate side-chains 127 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 5.263 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4489 time to fit residues: 15.9923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 359 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 116 optimal weight: 0.4980 chunk 382 optimal weight: 0.9980 chunk 409 optimal weight: 50.0000 chunk 297 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 432 HIS ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 48648 Z= 0.158 Angle : 0.491 7.473 66252 Z= 0.253 Chirality : 0.041 0.177 7644 Planarity : 0.004 0.084 8592 Dihedral : 4.268 21.300 6816 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.88 % Favored : 95.83 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6288 helix: 1.69 (0.14), residues: 1572 sheet: 1.53 (0.17), residues: 912 loop : -1.04 (0.10), residues: 3804 *********************** 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 143 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 6.167 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 142 average time/residue: 0.5586 time to fit residues: 146.0251 Evaluate side-chains 118 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 5.433 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4358 time to fit residues: 11.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 20.0000 chunk 576 optimal weight: 7.9990 chunk 525 optimal weight: 20.0000 chunk 560 optimal weight: 2.9990 chunk 337 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 506 optimal weight: 20.0000 chunk 530 optimal weight: 5.9990 chunk 558 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 432 HIS e 432 HIS f 432 HIS ** g 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 384 GLN ** 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: 0.8387 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 48648 Z= 0.254 Angle : 0.550 8.028 66252 Z= 0.287 Chirality : 0.042 0.194 7644 Planarity : 0.005 0.082 8592 Dihedral : 4.625 23.739 6816 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.38 % Favored : 94.31 % Rotamer Outliers : 0.18 % 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: 0.01 (0.11), residues: 6288 helix: 1.63 (0.14), residues: 1560 sheet: 1.68 (0.19), residues: 804 loop : -1.11 (0.10), residues: 3924 *********************** 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 127 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 5.038 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 126 average time/residue: 0.5118 time to fit residues: 117.7474 Evaluate side-chains 119 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 4.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4008 time to fit residues: 10.4303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 361 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 411 optimal weight: 4.9990 chunk 621 optimal weight: 7.9990 chunk 572 optimal weight: 20.0000 chunk 495 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 382 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 432 HIS ** g 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 48648 Z= 0.236 Angle : 0.542 10.738 66252 Z= 0.282 Chirality : 0.042 0.216 7644 Planarity : 0.005 0.081 8592 Dihedral : 4.629 23.277 6816 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.28 % Favored : 95.31 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 6288 helix: 1.60 (0.14), residues: 1560 sheet: 1.61 (0.19), residues: 804 loop : -1.15 (0.10), residues: 3924 ********************** 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 122 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 6.369 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.5337 time to fit residues: 119.7064 Evaluate side-chains 117 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 5.577 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4232 time to fit residues: 10.4601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 6.9990 chunk 527 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 456 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 495 optimal weight: 30.0000 chunk 207 optimal weight: 0.9990 chunk 509 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** d 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 432 HIS ** i 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045544 restraints weight = 250542.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046612 restraints weight = 138179.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.047337 restraints weight = 91221.493| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 48648 Z= 0.159 Angle : 0.499 11.159 66252 Z= 0.257 Chirality : 0.041 0.169 7644 Planarity : 0.004 0.083 8592 Dihedral : 4.319 21.456 6816 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.94 % Favored : 95.79 % Rotamer Outliers : 0.18 % 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: 1.70 (0.14), residues: 1572 sheet: 1.65 (0.19), residues: 804 loop : -1.09 (0.10), residues: 3912 =============================================================================== Job complete usr+sys time: 5724.27 seconds wall clock time: 108 minutes 49.90 seconds (6529.90 seconds total)