Starting phenix.real_space_refine on Sat Jul 4 02:23:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3p_15832/07_2026/8b3p_15832.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 115 5.16 5 C 11565 2.51 5 N 2750 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17620 Number of models: 1 Model: "" Number of chains: 55 Chain: "AAA" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "FFF" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "KKK" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "PPP" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "UUU" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ZZZ" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "eee" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "jjj" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ooo" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ttt" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "yyy" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BBB" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "GGG" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "LLL" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "QQQ" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "VVV" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "aaa" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "fff" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "kkk" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ppp" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "uuu" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "222" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CCC" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "HHH" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "MMM" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "RRR" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "WWW" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "bbb" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ggg" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "lll" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "qqq" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "vvv" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "111" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DDD" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "III" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "NNN" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "SSS" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "XXX" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ccc" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "hhh" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "mmm" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "rrr" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "www" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "zzz" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EEE" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "JJJ" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "OOO" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "TTT" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "YYY" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 339 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ddd" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "iii" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "nnn" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "sss" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "xxx" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "333" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 4.18, per 1000 atoms: 0.24 Number of scatterers: 17620 At special positions: 0 Unit cell: (79.2864, 80.3876, 224.645, 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 115 16.00 O 3190 8.00 N 2750 7.00 C 11565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 751.0 milliseconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 97.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'AAA' and resid 6 through 31 removed outlier: 3.559A pdb=" N ILEAAA 10 " --> pdb=" O ASPAAA 6 " (cutoff:3.500A) Processing helix chain 'FFF' and resid 2 through 32 removed outlier: 3.599A pdb=" N GLYFFF 14 " --> pdb=" O SERFFF 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGFFF 18 " --> pdb=" O GLYFFF 14 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEFFF 21 " --> pdb=" O LEUFFF 17 " (cutoff:3.500A) Processing helix chain 'KKK' and resid 6 through 50 removed outlier: 3.697A pdb=" N ALAKKK 16 " --> pdb=" O ASPKKK 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERKKK 17 " --> pdb=" O SERKKK 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAKKK 27 " --> pdb=" O GLYKKK 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALKKK 31 " --> pdb=" O ALAKKK 27 " (cutoff:3.500A) Processing helix chain 'PPP' and resid 7 through 50 removed outlier: 3.596A pdb=" N ALAPPP 27 " --> pdb=" O GLYPPP 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALPPP 31 " --> pdb=" O ALAPPP 27 " (cutoff:3.500A) Processing helix chain 'UUU' and resid 6 through 50 removed outlier: 3.579A pdb=" N ALAUUU 10 " --> pdb=" O PROUUU 6 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAUUU 27 " --> pdb=" O GLYUUU 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALUUU 31 " --> pdb=" O ALAUUU 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERUUU 47 " --> pdb=" O LYSUUU 43 " (cutoff:3.500A) Processing helix chain 'ZZZ' and resid 6 through 50 removed outlier: 3.574A pdb=" N ALAZZZ 10 " --> pdb=" O PROZZZ 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALZZZ 31 " --> pdb=" O ALAZZZ 27 " (cutoff:3.500A) Processing helix chain 'eee' and resid 6 through 50 removed outlier: 3.587A pdb=" N ALAeee 10 " --> pdb=" O PROeee 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALeee 31 " --> pdb=" O ALAeee 27 " (cutoff:3.500A) Processing helix chain 'jjj' and resid 6 through 50 removed outlier: 3.595A pdb=" N ALAjjj 10 " --> pdb=" O PROjjj 6 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALjjj 31 " --> pdb=" O ALAjjj 27 " (cutoff:3.500A) Processing helix chain 'ooo' and resid 6 through 50 removed outlier: 3.593A pdb=" N ALAooo 10 " --> pdb=" O PROooo 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAooo 27 " --> pdb=" O GLYooo 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALooo 31 " --> pdb=" O ALAooo 27 " (cutoff:3.500A) Processing helix chain 'ttt' and resid 6 through 50 removed outlier: 3.591A pdb=" N ALAttt 10 " --> pdb=" O PROttt 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAttt 27 " --> pdb=" O GLYttt 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALttt 31 " --> pdb=" O ALAttt 27 " (cutoff:3.500A) Processing helix chain 'yyy' and resid 6 through 50 removed outlier: 3.594A pdb=" N ALAyyy 10 " --> pdb=" O PROyyy 6 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALAyyy 27 " --> pdb=" O GLYyyy 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALyyy 31 " --> pdb=" O ALAyyy 27 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 7 through 31 Processing helix chain 'GGG' and resid 2 through 32 removed outlier: 3.599A pdb=" N GLYGGG 14 " --> pdb=" O SERGGG 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGGGG 18 " --> pdb=" O GLYGGG 14 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILEGGG 21 " --> pdb=" O LEUGGG 17 " (cutoff:3.500A) Processing helix chain 'LLL' and resid 6 through 50 removed outlier: 3.697A pdb=" N ALALLL 16 " --> pdb=" O ASPLLL 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERLLL 17 " --> pdb=" O SERLLL 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALALLL 27 " --> pdb=" O GLYLLL 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALLLL 31 " --> pdb=" O ALALLL 27 " (cutoff:3.500A) Processing helix chain 'QQQ' and resid 7 through 50 removed outlier: 3.596A pdb=" N ALAQQQ 27 " --> pdb=" O GLYQQQ 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALQQQ 31 " --> pdb=" O ALAQQQ 27 " (cutoff:3.500A) Processing helix chain 'VVV' and resid 6 through 50 removed outlier: 3.579A pdb=" N ALAVVV 10 " --> pdb=" O PROVVV 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAVVV 27 " --> pdb=" O GLYVVV 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALVVV 31 " --> pdb=" O ALAVVV 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERVVV 47 " --> pdb=" O LYSVVV 43 " (cutoff:3.500A) Processing helix chain 'aaa' and resid 6 through 50 removed outlier: 3.573A pdb=" N ALAaaa 10 " --> pdb=" O PROaaa 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALaaa 31 " --> pdb=" O ALAaaa 27 " (cutoff:3.500A) Processing helix chain 'fff' and resid 6 through 50 removed outlier: 3.588A pdb=" N ALAfff 10 " --> pdb=" O PROfff 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALfff 31 " --> pdb=" O ALAfff 27 " (cutoff:3.500A) Processing helix chain 'kkk' and resid 6 through 50 removed outlier: 3.594A pdb=" N ALAkkk 10 " --> pdb=" O PROkkk 6 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VALkkk 31 " --> pdb=" O ALAkkk 27 " (cutoff:3.500A) Processing helix chain 'ppp' and resid 6 through 50 removed outlier: 3.592A pdb=" N ALAppp 10 " --> pdb=" O PROppp 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAppp 27 " --> pdb=" O GLYppp 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALppp 31 " --> pdb=" O ALAppp 27 " (cutoff:3.500A) Processing helix chain 'uuu' and resid 6 through 50 removed outlier: 3.591A pdb=" N ALAuuu 10 " --> pdb=" O PROuuu 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAuuu 27 " --> pdb=" O GLYuuu 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALuuu 31 " --> pdb=" O ALAuuu 27 " (cutoff:3.500A) Processing helix chain '222' and resid 6 through 50 removed outlier: 3.595A pdb=" N ALA222 10 " --> pdb=" O PRO222 6 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA222 27 " --> pdb=" O GLY222 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL222 31 " --> pdb=" O ALA222 27 " (cutoff:3.500A) Processing helix chain 'CCC' and resid 7 through 31 Processing helix chain 'HHH' and resid 2 through 32 removed outlier: 3.599A pdb=" N GLYHHH 14 " --> pdb=" O SERHHH 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGHHH 18 " --> pdb=" O GLYHHH 14 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILEHHH 21 " --> pdb=" O LEUHHH 17 " (cutoff:3.500A) Processing helix chain 'MMM' and resid 6 through 50 removed outlier: 3.699A pdb=" N ALAMMM 16 " --> pdb=" O ASPMMM 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERMMM 17 " --> pdb=" O SERMMM 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALAMMM 27 " --> pdb=" O GLYMMM 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALMMM 31 " --> pdb=" O ALAMMM 27 " (cutoff:3.500A) Processing helix chain 'RRR' and resid 7 through 50 removed outlier: 3.596A pdb=" N ALARRR 27 " --> pdb=" O GLYRRR 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALRRR 31 " --> pdb=" O ALARRR 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERRRR 47 " --> pdb=" O LYSRRR 43 " (cutoff:3.500A) Processing helix chain 'WWW' and resid 6 through 50 removed outlier: 3.580A pdb=" N ALAWWW 10 " --> pdb=" O PROWWW 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAWWW 27 " --> pdb=" O GLYWWW 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALWWW 31 " --> pdb=" O ALAWWW 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERWWW 47 " --> pdb=" O LYSWWW 43 " (cutoff:3.500A) Processing helix chain 'bbb' and resid 6 through 50 removed outlier: 3.574A pdb=" N ALAbbb 10 " --> pdb=" O PRObbb 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALbbb 31 " --> pdb=" O ALAbbb 27 " (cutoff:3.500A) Processing helix chain 'ggg' and resid 6 through 50 removed outlier: 3.587A pdb=" N ALAggg 10 " --> pdb=" O PROggg 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALggg 31 " --> pdb=" O ALAggg 27 " (cutoff:3.500A) Processing helix chain 'lll' and resid 6 through 50 removed outlier: 3.592A pdb=" N ALAlll 10 " --> pdb=" O PROlll 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALlll 31 " --> pdb=" O ALAlll 27 " (cutoff:3.500A) Processing helix chain 'qqq' and resid 6 through 50 removed outlier: 3.592A pdb=" N ALAqqq 10 " --> pdb=" O PROqqq 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAqqq 27 " --> pdb=" O GLYqqq 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALqqq 31 " --> pdb=" O ALAqqq 27 " (cutoff:3.500A) Processing helix chain 'vvv' and resid 6 through 50 removed outlier: 3.591A pdb=" N ALAvvv 10 " --> pdb=" O PROvvv 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAvvv 27 " --> pdb=" O GLYvvv 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALvvv 31 " --> pdb=" O ALAvvv 27 " (cutoff:3.500A) Processing helix chain '111' and resid 6 through 50 removed outlier: 3.594A pdb=" N ALA111 10 " --> pdb=" O PRO111 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA111 27 " --> pdb=" O GLY111 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL111 31 " --> pdb=" O ALA111 27 " (cutoff:3.500A) Processing helix chain 'DDD' and resid 7 through 31 Processing helix chain 'III' and resid 2 through 32 removed outlier: 3.599A pdb=" N GLYIII 14 " --> pdb=" O SERIII 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGIII 18 " --> pdb=" O GLYIII 14 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILEIII 21 " --> pdb=" O LEUIII 17 " (cutoff:3.500A) Processing helix chain 'NNN' and resid 6 through 50 removed outlier: 3.698A pdb=" N ALANNN 16 " --> pdb=" O ASPNNN 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERNNN 17 " --> pdb=" O SERNNN 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALANNN 27 " --> pdb=" O GLYNNN 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALNNN 31 " --> pdb=" O ALANNN 27 " (cutoff:3.500A) Processing helix chain 'SSS' and resid 7 through 50 removed outlier: 3.597A pdb=" N ALASSS 27 " --> pdb=" O GLYSSS 23 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALSSS 31 " --> pdb=" O ALASSS 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERSSS 47 " --> pdb=" O LYSSSS 43 " (cutoff:3.500A) Processing helix chain 'XXX' and resid 6 through 50 removed outlier: 3.579A pdb=" N ALAXXX 10 " --> pdb=" O PROXXX 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAXXX 27 " --> pdb=" O GLYXXX 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALXXX 31 " --> pdb=" O ALAXXX 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERXXX 47 " --> pdb=" O LYSXXX 43 " (cutoff:3.500A) Processing helix chain 'ccc' and resid 6 through 50 removed outlier: 3.574A pdb=" N ALAccc 10 " --> pdb=" O PROccc 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALccc 31 " --> pdb=" O ALAccc 27 " (cutoff:3.500A) Processing helix chain 'hhh' and resid 6 through 50 removed outlier: 3.587A pdb=" N ALAhhh 10 " --> pdb=" O PROhhh 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALhhh 31 " --> pdb=" O ALAhhh 27 " (cutoff:3.500A) Processing helix chain 'mmm' and resid 6 through 50 removed outlier: 3.594A pdb=" N ALAmmm 10 " --> pdb=" O PROmmm 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALmmm 31 " --> pdb=" O ALAmmm 27 " (cutoff:3.500A) Processing helix chain 'rrr' and resid 6 through 50 removed outlier: 3.592A pdb=" N ALArrr 10 " --> pdb=" O PROrrr 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALArrr 27 " --> pdb=" O GLYrrr 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALrrr 31 " --> pdb=" O ALArrr 27 " (cutoff:3.500A) Processing helix chain 'www' and resid 6 through 50 removed outlier: 3.591A pdb=" N ALAwww 10 " --> pdb=" O PROwww 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAwww 27 " --> pdb=" O GLYwww 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALwww 31 " --> pdb=" O ALAwww 27 " (cutoff:3.500A) Processing helix chain 'zzz' and resid 6 through 50 removed outlier: 3.595A pdb=" N ALAzzz 10 " --> pdb=" O PROzzz 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAzzz 27 " --> pdb=" O GLYzzz 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALzzz 31 " --> pdb=" O ALAzzz 27 " (cutoff:3.500A) Processing helix chain 'EEE' and resid 7 through 31 Processing helix chain 'JJJ' and resid 2 through 32 removed outlier: 3.598A pdb=" N GLYJJJ 14 " --> pdb=" O SERJJJ 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARGJJJ 18 " --> pdb=" O GLYJJJ 14 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILEJJJ 21 " --> pdb=" O LEUJJJ 17 " (cutoff:3.500A) Processing helix chain 'OOO' and resid 6 through 50 removed outlier: 3.697A pdb=" N ALAOOO 16 " --> pdb=" O ASPOOO 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SEROOO 17 " --> pdb=" O SEROOO 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAOOO 27 " --> pdb=" O GLYOOO 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VALOOO 31 " --> pdb=" O ALAOOO 27 " (cutoff:3.500A) Processing helix chain 'TTT' and resid 7 through 50 removed outlier: 3.595A pdb=" N ALATTT 27 " --> pdb=" O GLYTTT 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALTTT 31 " --> pdb=" O ALATTT 27 " (cutoff:3.500A) Processing helix chain 'YYY' and resid 6 through 50 removed outlier: 3.578A pdb=" N ALAYYY 10 " --> pdb=" O PROYYY 6 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALAYYY 27 " --> pdb=" O GLYYYY 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALYYY 31 " --> pdb=" O ALAYYY 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERYYY 47 " --> pdb=" O LYSYYY 43 " (cutoff:3.500A) Processing helix chain 'ddd' and resid 6 through 50 removed outlier: 3.574A pdb=" N ALAddd 10 " --> pdb=" O PROddd 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALddd 31 " --> pdb=" O ALAddd 27 " (cutoff:3.500A) Processing helix chain 'iii' and resid 6 through 50 removed outlier: 3.587A pdb=" N ALAiii 10 " --> pdb=" O PROiii 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALiii 31 " --> pdb=" O ALAiii 27 " (cutoff:3.500A) Processing helix chain 'nnn' and resid 6 through 50 removed outlier: 3.594A pdb=" N ALAnnn 10 " --> pdb=" O PROnnn 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALnnn 31 " --> pdb=" O ALAnnn 27 " (cutoff:3.500A) Processing helix chain 'sss' and resid 6 through 50 removed outlier: 3.593A pdb=" N ALAsss 10 " --> pdb=" O PROsss 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAsss 27 " --> pdb=" O GLYsss 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALsss 31 " --> pdb=" O ALAsss 27 " (cutoff:3.500A) Processing helix chain 'xxx' and resid 6 through 50 removed outlier: 3.591A pdb=" N ALAxxx 10 " --> pdb=" O PROxxx 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAxxx 27 " --> pdb=" O GLYxxx 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALxxx 31 " --> pdb=" O ALAxxx 27 " (cutoff:3.500A) Processing helix chain '333' and resid 6 through 50 removed outlier: 3.595A pdb=" N ALA333 10 " --> pdb=" O PRO333 6 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA333 27 " --> pdb=" O GLY333 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL333 31 " --> pdb=" O ALA333 27 " (cutoff:3.500A) 1938 hydrogen bonds defined for protein. 5814 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: 3.65 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2940 1.34 - 1.46: 6528 1.46 - 1.58: 8242 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 17930 Sorted by residual: bond pdb=" N ASPttt 5 " pdb=" CA ASPttt 5 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.62e+00 bond pdb=" N ASPuuu 5 " pdb=" CA ASPuuu 5 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.59e+00 bond pdb=" N METJJJ 1 " pdb=" CA METJJJ 1 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.54e+00 bond pdb=" N ASPxxx 5 " pdb=" CA ASPxxx 5 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.53e+00 bond pdb=" N ASPwww 5 " pdb=" CA ASPwww 5 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.90e-02 2.77e+03 6.46e+00 ... (remaining 17925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 17409 1.56 - 3.12: 5607 3.12 - 4.67: 1032 4.67 - 6.23: 84 6.23 - 7.79: 53 Bond angle restraints: 24185 Sorted by residual: angle pdb=" C SERHHH 19 " pdb=" N GLYHHH 20 " pdb=" CA GLYHHH 20 " ideal model delta sigma weight residual 119.99 124.77 -4.78 1.13e+00 7.83e-01 1.79e+01 angle pdb=" C SERJJJ 19 " pdb=" N GLYJJJ 20 " pdb=" CA GLYJJJ 20 " ideal model delta sigma weight residual 119.99 124.77 -4.78 1.13e+00 7.83e-01 1.79e+01 angle pdb=" C SERGGG 19 " pdb=" N GLYGGG 20 " pdb=" CA GLYGGG 20 " ideal model delta sigma weight residual 119.99 124.76 -4.77 1.13e+00 7.83e-01 1.79e+01 angle pdb=" C SERFFF 19 " pdb=" N GLYFFF 20 " pdb=" CA GLYFFF 20 " ideal model delta sigma weight residual 119.99 124.76 -4.77 1.13e+00 7.83e-01 1.78e+01 angle pdb=" C SERIII 19 " pdb=" N GLYIII 20 " pdb=" CA GLYIII 20 " ideal model delta sigma weight residual 119.99 124.75 -4.76 1.13e+00 7.83e-01 1.77e+01 ... (remaining 24180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9316 17.82 - 35.64: 996 35.64 - 53.46: 143 53.46 - 71.28: 50 71.28 - 89.10: 60 Dihedral angle restraints: 10565 sinusoidal: 3770 harmonic: 6795 Sorted by residual: dihedral pdb=" C ASPaaa 5 " pdb=" N ASPaaa 5 " pdb=" CA ASPaaa 5 " pdb=" CB ASPaaa 5 " ideal model delta harmonic sigma weight residual -122.60 -133.05 10.45 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C ASPddd 5 " pdb=" N ASPddd 5 " pdb=" CA ASPddd 5 " pdb=" CB ASPddd 5 " ideal model delta harmonic sigma weight residual -122.60 -133.03 10.43 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C ASPiii 5 " pdb=" N ASPiii 5 " pdb=" CA ASPiii 5 " pdb=" CB ASPiii 5 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 10562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1565 0.074 - 0.147: 893 0.147 - 0.221: 319 0.221 - 0.295: 111 0.295 - 0.369: 12 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CA SERYYY 50 " pdb=" N SERYYY 50 " pdb=" C SERYYY 50 " pdb=" CB SERYYY 50 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA SERWWW 50 " pdb=" N SERWWW 50 " pdb=" C SERWWW 50 " pdb=" CB SERWWW 50 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA SERVVV 50 " pdb=" N SERVVV 50 " pdb=" C SERVVV 50 " pdb=" CB SERVVV 50 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2897 not shown) Planarity restraints: 2885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHESSS 11 " -0.025 2.00e-02 2.50e+03 1.66e-02 4.80e+00 pdb=" CG PHESSS 11 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHESSS 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHESSS 11 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHESSS 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHESSS 11 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESSS 11 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHETTT 11 " 0.024 2.00e-02 2.50e+03 1.64e-02 4.73e+00 pdb=" CG PHETTT 11 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHETTT 11 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHETTT 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHETTT 11 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHETTT 11 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHETTT 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHERRR 11 " -0.024 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHERRR 11 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHERRR 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHERRR 11 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHERRR 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHERRR 11 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHERRR 11 " -0.012 2.00e-02 2.50e+03 ... (remaining 2882 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 7335 2.95 - 3.44: 19519 3.44 - 3.93: 28253 3.93 - 4.41: 29670 4.41 - 4.90: 50182 Nonbonded interactions: 134959 Sorted by model distance: nonbonded pdb=" NE2 GLNQQQ 15 " pdb=" SD METMMM 28 " model vdw 2.469 3.480 nonbonded pdb=" NE2 GLNPPP 15 " pdb=" SD METLLL 28 " model vdw 2.482 3.480 nonbonded pdb=" NE2 GLNRRR 15 " pdb=" SD METNNN 28 " model vdw 2.486 3.480 nonbonded pdb=" SD METKKK 28 " pdb=" NE2 GLNTTT 15 " model vdw 2.499 3.480 nonbonded pdb=" NE2 GLNSSS 15 " pdb=" SD METOOO 28 " model vdw 2.504 3.480 ... (remaining 134954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain '111' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain '222' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain '333' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'KKK') selection = (chain 'LLL') selection = (chain 'MMM') selection = (chain 'NNN') selection = (chain 'OOO') selection = (chain 'PPP') selection = (chain 'QQQ') selection = (chain 'RRR') selection = (chain 'SSS') selection = (chain 'TTT') selection = (chain 'UUU') selection = (chain 'VVV') selection = (chain 'WWW') selection = (chain 'XXX') selection = (chain 'YYY') selection = (chain 'ZZZ' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'aaa' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'bbb' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ccc' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ddd' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'eee' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'fff' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ggg' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'hhh' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'iii' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'jjj' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'kkk' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'lll' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'mmm' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'nnn' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ooo' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ppp' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'qqq' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'rrr' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'sss' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'ttt' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'uuu' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'vvv' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'www' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'xxx' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'yyy' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) selection = (chain 'zzz' and (resid 5 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB or name OG )))) } ncs_group { reference = (chain 'AAA') selection = (chain 'BBB') selection = (chain 'CCC') selection = (chain 'DDD') selection = (chain 'EEE') } ncs_group { reference = (chain 'FFF') selection = (chain 'GGG') selection = (chain 'HHH') selection = (chain 'III') selection = (chain 'JJJ') } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.560 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9266 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 : 0.008 0.049 17930 Z= 0.497 Angle : 1.535 7.788 24185 Z= 1.081 Chirality : 0.103 0.369 2900 Planarity : 0.005 0.017 2885 Dihedral : 16.991 89.099 6145 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.78 % Allowed : 12.44 % Favored : 86.78 % Cbeta Deviations : 1.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 2260 helix: -0.36 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.01 (0.05), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGIII 18 TYR 0.015 0.004 TYRXXX 24 PHE 0.034 0.003 PHESSS 11 TRP 0.021 0.004 TRPQQQ 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.50 (17930) covalent geometry : angle 1.53473 / 1.08 (24185) hydrogen bonds : bond 0.27465 / 18.35 ( 1938) hydrogen bonds : angle 5.92321 / 4.35 ( 5814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 608 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AAA 33 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6878 (ttt180) REVERT: ZZZ 8 LYS cc_start: 0.9207 (tttm) cc_final: 0.8861 (tttp) REVERT: jjj 22 ILE cc_start: 0.9673 (mt) cc_final: 0.9440 (mp) REVERT: ooo 12 ASP cc_start: 0.9606 (m-30) cc_final: 0.9380 (m-30) REVERT: ttt 21 MET cc_start: 0.9472 (ttm) cc_final: 0.9257 (ttp) REVERT: yyy 20 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8973 (mp0) REVERT: BBB 33 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7405 (ttt180) REVERT: LLL 28 MET cc_start: 0.9166 (mmm) cc_final: 0.8964 (mmt) REVERT: aaa 8 LYS cc_start: 0.9139 (tttm) cc_final: 0.8857 (tttp) REVERT: fff 22 ILE cc_start: 0.9609 (mt) cc_final: 0.9398 (mt) REVERT: kkk 22 ILE cc_start: 0.9664 (mt) cc_final: 0.9414 (mt) REVERT: CCC 33 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7305 (ttt180) REVERT: qqq 8 LYS cc_start: 0.9607 (tttt) cc_final: 0.9378 (tttp) REVERT: qqq 12 ASP cc_start: 0.9611 (m-30) cc_final: 0.9265 (m-30) REVERT: qqq 41 LEU cc_start: 0.9803 (mt) cc_final: 0.9593 (mm) REVERT: 111 8 LYS cc_start: 0.9538 (tttt) cc_final: 0.9301 (tttm) REVERT: 111 12 ASP cc_start: 0.9511 (m-30) cc_final: 0.9277 (m-30) REVERT: DDD 33 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7199 (ttt-90) REVERT: NNN 21 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7792 (tmt) REVERT: ccc 8 LYS cc_start: 0.9177 (tttm) cc_final: 0.8848 (tttp) REVERT: rrr 8 LYS cc_start: 0.9614 (tttt) cc_final: 0.9405 (tttp) REVERT: rrr 12 ASP cc_start: 0.9607 (m-30) cc_final: 0.9337 (m-30) REVERT: EEE 33 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6846 (ttt180) REVERT: ddd 8 LYS cc_start: 0.9177 (tttm) cc_final: 0.8869 (tttp) REVERT: sss 12 ASP cc_start: 0.9622 (m-30) cc_final: 0.9388 (m-30) REVERT: 333 8 LYS cc_start: 0.9527 (tttt) cc_final: 0.9326 (tttm) outliers start: 14 outliers final: 1 residues processed: 613 average time/residue: 0.7045 time to fit residues: 472.4248 Evaluate side-chains 393 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 386 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 33 ARG Chi-restraints excluded: chain BBB residue 33 ARG Chi-restraints excluded: chain CCC residue 33 ARG Chi-restraints excluded: chain DDD residue 33 ARG Chi-restraints excluded: chain NNN residue 21 MET Chi-restraints excluded: chain EEE residue 33 ARG Chi-restraints excluded: chain OOO residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050424 restraints weight = 51633.959| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.50 r_work: 0.2991 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17930 Z= 0.182 Angle : 0.510 5.389 24185 Z= 0.288 Chirality : 0.035 0.173 2900 Planarity : 0.003 0.018 2885 Dihedral : 8.356 77.012 2446 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.94 % Allowed : 23.59 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.29 (0.15), residues: 2260 helix: 2.93 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -5.25 (0.69), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGGGG 26 TYR 0.007 0.001 TYRAAA 11 PHE 0.016 0.001 PHEddd 45 TRP 0.007 0.001 TRPLLL 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.18 (17930) covalent geometry : angle 0.50954 / 0.29 (24185) hydrogen bonds : bond 0.07864 / 5.19 ( 1938) hydrogen bonds : angle 3.49856 / 2.56 ( 5814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 500 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: KKK 13 SER cc_start: 0.9021 (t) cc_final: 0.8800 (p) REVERT: PPP 15 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8368 (mm110) REVERT: UUU 8 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7916 (ttmm) REVERT: jjj 22 ILE cc_start: 0.9404 (mt) cc_final: 0.9117 (mp) REVERT: yyy 12 ASP cc_start: 0.9225 (m-30) cc_final: 0.9015 (m-30) REVERT: yyy 44 LYS cc_start: 0.9751 (ttpt) cc_final: 0.9454 (ttpt) REVERT: BBB 12 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: fff 22 ILE cc_start: 0.9318 (mt) cc_final: 0.9105 (mt) REVERT: kkk 20 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8473 (mt-10) REVERT: 222 20 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8705 (mt-10) REVERT: CCC 12 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7850 (mm-40) REVERT: WWW 8 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8051 (ttmm) REVERT: lll 20 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8512 (mt-10) REVERT: 111 20 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8562 (mt-10) REVERT: NNN 13 SER cc_start: 0.9055 (t) cc_final: 0.8787 (p) REVERT: NNN 20 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: NNN 21 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7365 (tmt) REVERT: rrr 20 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8916 (mp0) REVERT: zzz 12 ASP cc_start: 0.9176 (m-30) cc_final: 0.8960 (m-30) REVERT: zzz 20 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8640 (mt-10) REVERT: ddd 22 ILE cc_start: 0.9133 (mt) cc_final: 0.8758 (mp) REVERT: nnn 8 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7594 (ttpp) REVERT: nnn 20 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8384 (mt-10) outliers start: 106 outliers final: 5 residues processed: 544 average time/residue: 0.5915 time to fit residues: 356.1146 Evaluate side-chains 340 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 331 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BBB residue 12 GLN Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain CCC residue 12 GLN Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 21 MET Chi-restraints excluded: chain nnn residue 41 LEU Chi-restraints excluded: chain 333 residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 144 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050630 restraints weight = 53676.913| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.63 r_work: 0.2904 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17930 Z= 0.168 Angle : 0.473 6.462 24185 Z= 0.258 Chirality : 0.033 0.108 2900 Planarity : 0.002 0.013 2885 Dihedral : 7.078 66.327 2423 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 27.51 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.65 (0.15), residues: 2260 helix: 3.78 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.74 (0.61), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGGGG 26 TYR 0.007 0.001 TYRDDD 11 PHE 0.015 0.001 PHESSS 11 TRP 0.006 0.001 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (17930) covalent geometry : angle 0.47299 / 0.26 (24185) hydrogen bonds : bond 0.07788 / 5.16 ( 1938) hydrogen bonds : angle 3.44465 / 2.52 ( 5814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 391 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PPP 15 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8553 (mt0) REVERT: jjj 47 SER cc_start: 0.9442 (t) cc_final: 0.8958 (p) REVERT: BBB 12 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (mm-40) REVERT: QQQ 11 PHE cc_start: 0.6509 (t80) cc_final: 0.6133 (t80) REVERT: kkk 48 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8882 (tppp) REVERT: RRR 5 ASP cc_start: 0.6526 (p0) cc_final: 0.6051 (t70) REVERT: RRR 11 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5873 (t80) REVERT: 111 45 PHE cc_start: 0.9543 (m-80) cc_final: 0.9312 (m-80) REVERT: DDD 15 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8231 (mm) REVERT: NNN 20 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: zzz 12 ASP cc_start: 0.9178 (m-30) cc_final: 0.8944 (m-30) REVERT: zzz 20 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8563 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9574 (m-80) cc_final: 0.9335 (m-80) REVERT: TTT 5 ASP cc_start: 0.6476 (p0) cc_final: 0.6208 (p0) REVERT: sss 20 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8937 (mp0) outliers start: 70 outliers final: 9 residues processed: 418 average time/residue: 0.6926 time to fit residues: 317.6190 Evaluate side-chains 349 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 334 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BBB residue 12 GLN Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain fff residue 21 MET Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain kkk residue 48 LYS Chi-restraints excluded: chain RRR residue 11 PHE Chi-restraints excluded: chain qqq residue 21 MET Chi-restraints excluded: chain DDD residue 15 ILE Chi-restraints excluded: chain III residue 31 SER Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain OOO residue 33 VAL Chi-restraints excluded: chain nnn residue 41 LEU Chi-restraints excluded: chain sss residue 20 GLU Chi-restraints excluded: chain 333 residue 41 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050249 restraints weight = 53523.592| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.64 r_work: 0.2882 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17930 Z= 0.167 Angle : 0.464 6.774 24185 Z= 0.253 Chirality : 0.032 0.109 2900 Planarity : 0.002 0.021 2885 Dihedral : 6.605 75.229 2420 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.91 % Allowed : 29.69 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.88 (0.15), residues: 2260 helix: 3.93 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.67 (0.59), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGGGG 26 TYR 0.007 0.001 TYRGGG 6 PHE 0.015 0.001 PHERRR 11 TRP 0.007 0.001 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (17930) covalent geometry : angle 0.46418 / 0.25 (24185) hydrogen bonds : bond 0.07682 / 5.09 ( 1938) hydrogen bonds : angle 3.46775 / 2.54 ( 5814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: jjj 47 SER cc_start: 0.9442 (t) cc_final: 0.8975 (p) REVERT: jjj 48 LYS cc_start: 0.9294 (tptt) cc_final: 0.9030 (tppp) REVERT: ooo 44 LYS cc_start: 0.9694 (tppp) cc_final: 0.9377 (tppp) REVERT: BBB 12 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7847 (mm-40) REVERT: kkk 48 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8887 (tppp) REVERT: ppp 44 LYS cc_start: 0.9644 (tppp) cc_final: 0.9240 (tppp) REVERT: lll 20 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8408 (mt-10) REVERT: 111 45 PHE cc_start: 0.9542 (m-80) cc_final: 0.9322 (m-80) REVERT: NNN 20 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: SSS 11 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5812 (t80) REVERT: mmm 44 LYS cc_start: 0.9704 (OUTLIER) cc_final: 0.9454 (ttpt) REVERT: zzz 12 ASP cc_start: 0.9155 (m-30) cc_final: 0.8911 (m-30) REVERT: zzz 45 PHE cc_start: 0.9562 (m-80) cc_final: 0.9222 (m-80) REVERT: TTT 15 GLN cc_start: 0.8789 (mm110) cc_final: 0.8445 (mt0) REVERT: nnn 20 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8821 (mt-10) REVERT: sss 20 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8982 (mp0) outliers start: 52 outliers final: 11 residues processed: 398 average time/residue: 0.6661 time to fit residues: 291.8677 Evaluate side-chains 352 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 335 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 33 VAL Chi-restraints excluded: chain ooo residue 39 ILE Chi-restraints excluded: chain yyy residue 41 LEU Chi-restraints excluded: chain BBB residue 12 GLN Chi-restraints excluded: chain GGG residue 31 SER Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 28 MET Chi-restraints excluded: chain kkk residue 48 LYS Chi-restraints excluded: chain MMM residue 22 ILE Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 33 VAL Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 50 SER Chi-restraints excluded: chain mmm residue 44 LYS Chi-restraints excluded: chain rrr residue 39 ILE Chi-restraints excluded: chain sss residue 20 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 41 optimal weight: 0.0270 chunk 200 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050705 restraints weight = 53721.530| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.64 r_work: 0.2902 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17930 Z= 0.162 Angle : 0.475 8.258 24185 Z= 0.256 Chirality : 0.032 0.108 2900 Planarity : 0.002 0.027 2885 Dihedral : 6.402 71.828 2420 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.24 % Allowed : 30.70 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.12 (0.15), residues: 2260 helix: 4.07 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.19 (0.64), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGIII 26 TYR 0.007 0.001 TYRGGG 6 PHE 0.012 0.001 PHESSS 11 TRP 0.005 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (17930) covalent geometry : angle 0.47465 / 0.26 (24185) hydrogen bonds : bond 0.07362 / 4.88 ( 1938) hydrogen bonds : angle 3.42755 / 2.51 ( 5814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: jjj 48 LYS cc_start: 0.9271 (tptt) cc_final: 0.9034 (tppp) REVERT: ooo 44 LYS cc_start: 0.9700 (tppp) cc_final: 0.9378 (tppp) REVERT: kkk 48 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8884 (tppp) REVERT: ppp 44 LYS cc_start: 0.9668 (tppp) cc_final: 0.9191 (tppp) REVERT: ppp 48 LYS cc_start: 0.8994 (tptt) cc_final: 0.8546 (tppp) REVERT: lll 20 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8388 (mt-10) REVERT: 111 45 PHE cc_start: 0.9508 (m-80) cc_final: 0.9274 (m-80) REVERT: NNN 20 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: SSS 11 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.5220 (t80) REVERT: SSS 15 GLN cc_start: 0.7962 (mt0) cc_final: 0.7643 (pm20) REVERT: rrr 44 LYS cc_start: 0.9701 (tppp) cc_final: 0.9252 (tppp) REVERT: zzz 12 ASP cc_start: 0.9142 (m-30) cc_final: 0.8914 (m-30) REVERT: zzz 20 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8453 (mp0) REVERT: TTT 15 GLN cc_start: 0.8912 (mm110) cc_final: 0.8494 (mt0) REVERT: sss 20 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8986 (mp0) REVERT: sss 44 LYS cc_start: 0.9705 (tppp) cc_final: 0.9266 (OUTLIER) outliers start: 40 outliers final: 14 residues processed: 386 average time/residue: 0.6524 time to fit residues: 276.7407 Evaluate side-chains 355 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 338 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 33 VAL Chi-restraints excluded: chain KKK residue 44 LYS Chi-restraints excluded: chain ooo residue 39 ILE Chi-restraints excluded: chain yyy residue 41 LEU Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 28 MET Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain kkk residue 48 LYS Chi-restraints excluded: chain MMM residue 22 ILE Chi-restraints excluded: chain III residue 31 SER Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 33 VAL Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 22 ILE Chi-restraints excluded: chain sss residue 20 GLU Chi-restraints excluded: chain 333 residue 41 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 64 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049799 restraints weight = 53382.287| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.64 r_work: 0.2896 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17930 Z= 0.165 Angle : 0.488 9.476 24185 Z= 0.263 Chirality : 0.033 0.107 2900 Planarity : 0.002 0.021 2885 Dihedral : 6.204 69.931 2420 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.69 % Allowed : 31.04 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.10 (0.15), residues: 2260 helix: 4.05 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -3.81 (0.65), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGIII 26 TYR 0.007 0.001 TYRGGG 6 PHE 0.012 0.001 PHESSS 11 TRP 0.005 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (17930) covalent geometry : angle 0.48764 / 0.26 (24185) hydrogen bonds : bond 0.07426 / 4.93 ( 1938) hydrogen bonds : angle 3.47066 / 2.54 ( 5814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 355 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: UUU 14 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8606 (mp) REVERT: jjj 48 LYS cc_start: 0.9277 (tptt) cc_final: 0.9040 (tppp) REVERT: ooo 44 LYS cc_start: 0.9720 (tppp) cc_final: 0.9361 (tppp) REVERT: ooo 48 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8635 (tppp) REVERT: kkk 48 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8909 (tppp) REVERT: ppp 44 LYS cc_start: 0.9701 (tppp) cc_final: 0.9244 (tppp) REVERT: ppp 48 LYS cc_start: 0.9028 (tptt) cc_final: 0.8577 (tppp) REVERT: lll 20 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8391 (mt-10) REVERT: NNN 20 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: SSS 11 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.4952 (t80) REVERT: SSS 15 GLN cc_start: 0.7948 (mt0) cc_final: 0.7539 (mp10) REVERT: rrr 44 LYS cc_start: 0.9706 (tppp) cc_final: 0.9268 (tppp) REVERT: zzz 12 ASP cc_start: 0.9143 (m-30) cc_final: 0.8888 (m-30) REVERT: zzz 20 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8505 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9486 (m-80) cc_final: 0.9182 (m-80) REVERT: TTT 15 GLN cc_start: 0.8957 (mm110) cc_final: 0.8551 (mt0) REVERT: nnn 20 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8764 (mt-10) REVERT: sss 20 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8933 (mp0) REVERT: sss 44 LYS cc_start: 0.9719 (tppp) cc_final: 0.9298 (tppp) outliers start: 48 outliers final: 16 residues processed: 373 average time/residue: 0.7116 time to fit residues: 291.1896 Evaluate side-chains 354 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 44 LYS Chi-restraints excluded: chain KKK residue 50 SER Chi-restraints excluded: chain UUU residue 14 LEU Chi-restraints excluded: chain ooo residue 48 LYS Chi-restraints excluded: chain yyy residue 41 LEU Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain LLL residue 50 SER Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 28 MET Chi-restraints excluded: chain kkk residue 31 VAL Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain kkk residue 48 LYS Chi-restraints excluded: chain MMM residue 22 ILE Chi-restraints excluded: chain 111 residue 41 LEU Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 33 VAL Chi-restraints excluded: chain NNN residue 50 SER Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 50 SER Chi-restraints excluded: chain XXX residue 21 MET Chi-restraints excluded: chain sss residue 20 GLU Chi-restraints excluded: chain sss residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 144 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046171 restraints weight = 53444.729| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.58 r_work: 0.2881 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17930 Z= 0.171 Angle : 0.501 9.172 24185 Z= 0.270 Chirality : 0.033 0.109 2900 Planarity : 0.002 0.020 2885 Dihedral : 6.051 66.455 2420 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.24 % Allowed : 31.37 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.03 (0.15), residues: 2260 helix: 4.01 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -3.70 (0.65), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGIII 26 TYR 0.007 0.001 TYRGGG 6 PHE 0.013 0.001 PHESSS 11 TRP 0.005 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (17930) covalent geometry : angle 0.50122 / 0.27 (24185) hydrogen bonds : bond 0.07624 / 5.06 ( 1938) hydrogen bonds : angle 3.52240 / 2.57 ( 5814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 0.720 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: UUU 14 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8579 (mp) REVERT: jjj 48 LYS cc_start: 0.9288 (tptt) cc_final: 0.9040 (tppp) REVERT: ooo 44 LYS cc_start: 0.9715 (tppp) cc_final: 0.9363 (tppp) REVERT: ooo 48 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8642 (tppp) REVERT: kkk 48 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8907 (tppp) REVERT: ppp 44 LYS cc_start: 0.9699 (tppp) cc_final: 0.9236 (tppp) REVERT: ppp 48 LYS cc_start: 0.9028 (tptt) cc_final: 0.8569 (tppp) REVERT: 111 20 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8623 (mt-10) REVERT: 111 45 PHE cc_start: 0.9441 (m-80) cc_final: 0.9240 (m-80) REVERT: NNN 20 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: SSS 11 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5064 (t80) REVERT: SSS 15 GLN cc_start: 0.7990 (mt0) cc_final: 0.7575 (mp10) REVERT: hhh 21 MET cc_start: 0.9239 (mmt) cc_final: 0.8933 (tpp) REVERT: rrr 44 LYS cc_start: 0.9700 (tppp) cc_final: 0.9314 (tppp) REVERT: zzz 12 ASP cc_start: 0.9154 (m-30) cc_final: 0.8887 (m-30) REVERT: zzz 20 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8548 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9512 (m-80) cc_final: 0.9186 (m-80) REVERT: TTT 15 GLN cc_start: 0.8953 (mm110) cc_final: 0.8491 (mp10) REVERT: sss 20 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8918 (mp0) REVERT: sss 44 LYS cc_start: 0.9700 (tppp) cc_final: 0.9231 (tppp) REVERT: sss 48 LYS cc_start: 0.9100 (tptt) cc_final: 0.8591 (tppp) outliers start: 40 outliers final: 15 residues processed: 363 average time/residue: 0.7311 time to fit residues: 291.3710 Evaluate side-chains 355 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 50 SER Chi-restraints excluded: chain UUU residue 14 LEU Chi-restraints excluded: chain ooo residue 48 LYS Chi-restraints excluded: chain yyy residue 41 LEU Chi-restraints excluded: chain LLL residue 17 SER Chi-restraints excluded: chain LLL residue 50 SER Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 31 VAL Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain kkk residue 48 LYS Chi-restraints excluded: chain MMM residue 22 ILE Chi-restraints excluded: chain III residue 31 SER Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 33 VAL Chi-restraints excluded: chain NNN residue 50 SER Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 22 ILE Chi-restraints excluded: chain SSS residue 50 SER Chi-restraints excluded: chain XXX residue 21 MET Chi-restraints excluded: chain mmm residue 31 VAL Chi-restraints excluded: chain sss residue 20 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 132 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 174 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052404 restraints weight = 53246.964| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.62 r_work: 0.2945 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17930 Z= 0.157 Angle : 0.500 11.511 24185 Z= 0.267 Chirality : 0.033 0.120 2900 Planarity : 0.002 0.019 2885 Dihedral : 6.127 72.833 2420 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 31.65 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.37 (0.15), residues: 2260 helix: 4.32 (0.09), residues: 2175 sheet: None (None), residues: 0 loop : -2.78 (0.36), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGIII 26 TYR 0.006 0.001 TYRjjj 24 PHE 0.011 0.001 PHESSS 11 TRP 0.004 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (17930) covalent geometry : angle 0.49966 / 0.27 (24185) hydrogen bonds : bond 0.06807 / 4.51 ( 1938) hydrogen bonds : angle 3.40228 / 2.49 ( 5814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 0.504 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: jjj 20 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: jjj 47 SER cc_start: 0.9327 (t) cc_final: 0.8848 (p) REVERT: jjj 48 LYS cc_start: 0.9207 (tptt) cc_final: 0.8977 (tppp) REVERT: ooo 44 LYS cc_start: 0.9714 (tppp) cc_final: 0.9384 (tppp) REVERT: ooo 48 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8645 (tppp) REVERT: ppp 44 LYS cc_start: 0.9698 (tppp) cc_final: 0.9246 (tppp) REVERT: ppp 48 LYS cc_start: 0.8970 (tptt) cc_final: 0.8519 (tppp) REVERT: uuu 40 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9335 (tttt) REVERT: 222 45 PHE cc_start: 0.9460 (m-80) cc_final: 0.9116 (m-80) REVERT: MMM 20 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: lll 20 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8724 (mt-10) REVERT: qqq 44 LYS cc_start: 0.9656 (tppp) cc_final: 0.9286 (OUTLIER) REVERT: 111 20 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8603 (mt-10) REVERT: 111 45 PHE cc_start: 0.9435 (m-80) cc_final: 0.9214 (m-80) REVERT: NNN 20 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: SSS 11 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5151 (t80) REVERT: SSS 15 GLN cc_start: 0.7985 (mt0) cc_final: 0.7715 (mp10) REVERT: mmm 20 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8294 (mp0) REVERT: rrr 44 LYS cc_start: 0.9701 (tppp) cc_final: 0.9261 (tppp) REVERT: rrr 48 LYS cc_start: 0.9032 (tptt) cc_final: 0.8550 (tppp) REVERT: zzz 20 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8534 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9452 (m-80) cc_final: 0.9144 (m-80) REVERT: TTT 15 GLN cc_start: 0.8936 (mm110) cc_final: 0.8492 (mp10) REVERT: sss 20 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8934 (mp0) REVERT: sss 40 LYS cc_start: 0.9725 (tmtt) cc_final: 0.9502 (tmmm) REVERT: sss 44 LYS cc_start: 0.9687 (tppp) cc_final: 0.9236 (tppp) REVERT: sss 48 LYS cc_start: 0.9091 (tptt) cc_final: 0.8614 (tppp) REVERT: 333 45 PHE cc_start: 0.9438 (m-80) cc_final: 0.9075 (m-80) outliers start: 35 outliers final: 12 residues processed: 384 average time/residue: 0.6824 time to fit residues: 288.0986 Evaluate side-chains 353 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 336 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 50 SER Chi-restraints excluded: chain jjj residue 20 GLU Chi-restraints excluded: chain ooo residue 48 LYS Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 31 VAL Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain MMM residue 20 GLU Chi-restraints excluded: chain WWW residue 14 LEU Chi-restraints excluded: chain III residue 31 SER Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain NNN residue 33 VAL Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 22 ILE Chi-restraints excluded: chain XXX residue 21 MET Chi-restraints excluded: chain mmm residue 31 VAL Chi-restraints excluded: chain OOO residue 50 SER Chi-restraints excluded: chain sss residue 20 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 144 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050800 restraints weight = 53671.894| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.65 r_work: 0.2921 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17930 Z= 0.164 Angle : 0.521 10.792 24185 Z= 0.278 Chirality : 0.033 0.210 2900 Planarity : 0.002 0.019 2885 Dihedral : 6.012 74.281 2420 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.57 % Allowed : 31.99 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.09 (0.16), residues: 2260 helix: 4.04 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -3.70 (0.61), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGIII 26 TYR 0.006 0.001 TYRGGG 6 PHE 0.012 0.001 PHESSS 11 TRP 0.004 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (17930) covalent geometry : angle 0.52089 / 0.28 (24185) hydrogen bonds : bond 0.07086 / 4.70 ( 1938) hydrogen bonds : angle 3.51394 / 2.57 ( 5814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 355 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PPP 21 MET cc_start: 0.9008 (mtt) cc_final: 0.8806 (mtt) REVERT: jjj 20 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: ooo 44 LYS cc_start: 0.9718 (tppp) cc_final: 0.9391 (tppp) REVERT: ooo 48 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8634 (tppp) REVERT: LLL 29 VAL cc_start: 0.9304 (p) cc_final: 0.9092 (p) REVERT: ppp 44 LYS cc_start: 0.9693 (tppp) cc_final: 0.9254 (tppp) REVERT: ppp 48 LYS cc_start: 0.8977 (tptt) cc_final: 0.8522 (tppp) REVERT: uuu 40 LYS cc_start: 0.9577 (ttmt) cc_final: 0.9351 (tttt) REVERT: 222 45 PHE cc_start: 0.9442 (m-80) cc_final: 0.9095 (m-80) REVERT: MMM 20 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: lll 20 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8718 (mt-10) REVERT: qqq 44 LYS cc_start: 0.9658 (tppp) cc_final: 0.9286 (OUTLIER) REVERT: 111 45 PHE cc_start: 0.9432 (m-80) cc_final: 0.9193 (m-80) REVERT: NNN 20 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: SSS 11 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5317 (t80) REVERT: SSS 15 GLN cc_start: 0.8020 (mt0) cc_final: 0.7749 (mp10) REVERT: mmm 20 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8388 (mp0) REVERT: rrr 44 LYS cc_start: 0.9707 (tppp) cc_final: 0.9269 (tppp) REVERT: rrr 48 LYS cc_start: 0.9039 (tptt) cc_final: 0.8550 (tppp) REVERT: zzz 20 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8523 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9469 (m-80) cc_final: 0.9159 (m-80) REVERT: JJJ 28 MET cc_start: 0.8923 (tpp) cc_final: 0.8674 (ttt) REVERT: TTT 15 GLN cc_start: 0.8975 (mm110) cc_final: 0.8622 (mp10) REVERT: sss 20 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8961 (mp0) REVERT: sss 40 LYS cc_start: 0.9735 (tmtt) cc_final: 0.9501 (tmmm) REVERT: sss 44 LYS cc_start: 0.9684 (tppp) cc_final: 0.9225 (tppp) REVERT: sss 48 LYS cc_start: 0.9064 (tptt) cc_final: 0.8587 (tppp) REVERT: 333 45 PHE cc_start: 0.9442 (m-80) cc_final: 0.9142 (m-80) outliers start: 28 outliers final: 10 residues processed: 370 average time/residue: 0.6393 time to fit residues: 259.7713 Evaluate side-chains 350 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 335 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain KKK residue 50 SER Chi-restraints excluded: chain jjj residue 20 GLU Chi-restraints excluded: chain jjj residue 41 LEU Chi-restraints excluded: chain ooo residue 48 LYS Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 31 VAL Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain MMM residue 20 GLU Chi-restraints excluded: chain III residue 31 SER Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 22 ILE Chi-restraints excluded: chain mmm residue 31 VAL Chi-restraints excluded: chain OOO residue 50 SER Chi-restraints excluded: chain sss residue 20 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 106 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 25 optimal weight: 0.0070 chunk 134 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.069175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051869 restraints weight = 53339.860| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.62 r_work: 0.2948 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17930 Z= 0.159 Angle : 0.524 10.138 24185 Z= 0.279 Chirality : 0.033 0.162 2900 Planarity : 0.002 0.019 2885 Dihedral : 6.015 74.579 2420 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.90 % Allowed : 33.11 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.24 (0.15), residues: 2260 helix: 4.24 (0.09), residues: 2175 sheet: None (None), residues: 0 loop : -2.68 (0.35), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGIII 26 TYR 0.006 0.001 TYRGGG 6 PHE 0.014 0.001 PHE222 45 TRP 0.004 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (17930) covalent geometry : angle 0.52423 / 0.28 (24185) hydrogen bonds : bond 0.06790 / 4.50 ( 1938) hydrogen bonds : angle 3.47025 / 2.54 ( 5814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 351 time to evaluate : 0.847 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: jjj 20 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: jjj 47 SER cc_start: 0.9319 (t) cc_final: 0.8835 (p) REVERT: ooo 44 LYS cc_start: 0.9712 (tppp) cc_final: 0.9351 (tppp) REVERT: ooo 48 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (tppp) REVERT: LLL 29 VAL cc_start: 0.9295 (p) cc_final: 0.9080 (p) REVERT: ppp 44 LYS cc_start: 0.9678 (tppp) cc_final: 0.9262 (tppp) REVERT: ppp 48 LYS cc_start: 0.8945 (tptt) cc_final: 0.8501 (tppp) REVERT: uuu 40 LYS cc_start: 0.9557 (ttmt) cc_final: 0.9327 (tttt) REVERT: 222 20 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8608 (mp0) REVERT: 222 45 PHE cc_start: 0.9441 (m-80) cc_final: 0.9135 (m-80) REVERT: HHH 28 MET cc_start: 0.8457 (tpp) cc_final: 0.8246 (mmp) REVERT: MMM 20 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: lll 20 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8712 (mt-10) REVERT: lll 47 SER cc_start: 0.9174 (t) cc_final: 0.8764 (p) REVERT: qqq 44 LYS cc_start: 0.9663 (tppp) cc_final: 0.9349 (OUTLIER) REVERT: 111 45 PHE cc_start: 0.9420 (m-80) cc_final: 0.9098 (m-80) REVERT: SSS 11 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5594 (t80) REVERT: SSS 15 GLN cc_start: 0.8002 (mt0) cc_final: 0.7735 (mp10) REVERT: rrr 44 LYS cc_start: 0.9711 (tppp) cc_final: 0.9273 (tppp) REVERT: rrr 48 LYS cc_start: 0.9009 (tptt) cc_final: 0.8520 (tppp) REVERT: zzz 20 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8525 (mt-10) REVERT: zzz 45 PHE cc_start: 0.9449 (m-80) cc_final: 0.9164 (m-80) REVERT: JJJ 28 MET cc_start: 0.8929 (tpp) cc_final: 0.8644 (ttt) REVERT: TTT 11 PHE cc_start: 0.6605 (t80) cc_final: 0.5711 (t80) REVERT: TTT 15 GLN cc_start: 0.8876 (mm110) cc_final: 0.8551 (mp10) REVERT: nnn 20 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8347 (mp0) REVERT: sss 20 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: sss 40 LYS cc_start: 0.9741 (tmtt) cc_final: 0.9525 (tmmm) REVERT: sss 44 LYS cc_start: 0.9688 (tppp) cc_final: 0.9216 (tppp) REVERT: sss 48 LYS cc_start: 0.8992 (tptt) cc_final: 0.8512 (tppp) REVERT: 333 45 PHE cc_start: 0.9461 (m-80) cc_final: 0.9169 (m-80) outliers start: 16 outliers final: 10 residues processed: 356 average time/residue: 0.7220 time to fit residues: 282.1888 Evaluate side-chains 351 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 337 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain jjj residue 20 GLU Chi-restraints excluded: chain ooo residue 48 LYS Chi-restraints excluded: chain ttt residue 44 LYS Chi-restraints excluded: chain kkk residue 21 MET Chi-restraints excluded: chain kkk residue 31 VAL Chi-restraints excluded: chain kkk residue 41 LEU Chi-restraints excluded: chain MMM residue 20 GLU Chi-restraints excluded: chain WWW residue 14 LEU Chi-restraints excluded: chain NNN residue 20 GLU Chi-restraints excluded: chain SSS residue 11 PHE Chi-restraints excluded: chain SSS residue 22 ILE Chi-restraints excluded: chain XXX residue 21 MET Chi-restraints excluded: chain mmm residue 31 VAL Chi-restraints excluded: chain sss residue 20 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 195 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.069221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051969 restraints weight = 53725.666| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.63 r_work: 0.2937 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17930 Z= 0.161 Angle : 0.529 10.044 24185 Z= 0.280 Chirality : 0.033 0.230 2900 Planarity : 0.002 0.020 2885 Dihedral : 5.972 74.439 2420 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.18 % Allowed : 33.05 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.06 (0.16), residues: 2260 helix: 4.02 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -3.66 (0.61), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGIII 26 TYR 0.006 0.001 TYRGGG 6 PHE 0.014 0.001 PHE222 45 TRP 0.004 0.000 TRPTTT 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (17930) covalent geometry : angle 0.52882 / 0.28 (24185) hydrogen bonds : bond 0.06883 / 4.56 ( 1938) hydrogen bonds : angle 3.50459 / 2.57 ( 5814) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6077.46 seconds wall clock time: 103 minutes 51.97 seconds (6231.97 seconds total)