Starting phenix.real_space_refine on Fri Nov 17 02:42:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Bad HELIX record, was skipped: HELIX 1 AA1 ASPAAA 6 GLYAAA 31 1 26 Bad HELIX record, was skipped: HELIX 2 AA2 SERFFF 2 SERFFF 32 1 31 Bad HELIX record, was skipped: HELIX 3 AA3 PROKKK 6 SERKKK 50 1 45 Bad HELIX record, was skipped: HELIX 4 AA4 ALAPPP 7 SERPPP 50 1 44 Bad HELIX record, was skipped: HELIX 5 AA5 PROUUU 6 SERUUU 50 1 45 Bad HELIX record, was skipped: HELIX 6 AA6 PROZZZ 6 SERZZZ 50 1 45 Bad HELIX record, was skipped: HELIX 7 AA7 PROeee 6 SEReee 50 1 45 Bad HELIX record, was skipped: HELIX 8 AA8 PROjjj 6 SERjjj 50 1 45 Bad HELIX record, was skipped: HELIX 9 AA9 PROooo 6 SERooo 50 1 45 Bad HELIX record, was skipped: HELIX 10 AB1 PROttt 6 SERttt 50 1 45 Bad HELIX record, was skipped: HELIX 11 AB2 PROyyy 6 SERyyy 50 1 45 Bad HELIX record, was skipped: HELIX 12 AB3 PHEBBB 7 GLYBBB 31 1 25 Bad HELIX record, was skipped: HELIX 13 AB4 SERGGG 2 SERGGG 32 1 31 Bad HELIX record, was skipped: HELIX 14 AB5 PROLLL 6 SERLLL 50 1 45 Bad HELIX record, was skipped: HELIX 15 AB6 ALAQQQ 7 SERQQQ 50 1 44 Bad HELIX record, was skipped: HELIX 16 AB7 PROVVV 6 SERVVV 50 1 45 Bad HELIX record, was skipped: HELIX 17 AB8 PROaaa 6 SERaaa 50 1 45 Bad HELIX record, was skipped: HELIX 18 AB9 PROfff 6 SERfff 50 1 45 Bad HELIX record, was skipped: HELIX 19 AC1 PROkkk 6 SERkkk 50 1 45 Bad HELIX record, was skipped: HELIX 20 AC2 PROppp 6 SERppp 50 1 45 Bad HELIX record, was skipped: HELIX 21 AC3 PROuuu 6 SERuuu 50 1 45 Bad HELIX record, was skipped: HELIX 22 AC4 PRO222 6 SER222 50 1 45 Bad HELIX record, was skipped: HELIX 23 AC5 PHECCC 7 GLYCCC 31 1 25 Bad HELIX record, was skipped: HELIX 24 AC6 SERHHH 2 SERHHH 32 1 31 Bad HELIX record, was skipped: HELIX 25 AC7 PROMMM 6 SERMMM 50 1 45 Bad HELIX record, was skipped: HELIX 26 AC8 ALARRR 7 SERRRR 50 1 44 Bad HELIX record, was skipped: HELIX 27 AC9 PROWWW 6 SERWWW 50 1 45 Bad HELIX record, was skipped: HELIX 28 AD1 PRObbb 6 SERbbb 50 1 45 Bad HELIX record, was skipped: HELIX 29 AD2 PROggg 6 SERggg 50 1 45 Bad HELIX record, was skipped: HELIX 30 AD3 PROlll 6 SERlll 50 1 45 Bad HELIX record, was skipped: HELIX 31 AD4 PROqqq 6 SERqqq 50 1 45 Bad HELIX record, was skipped: HELIX 32 AD5 PROvvv 6 SERvvv 50 1 45 Bad HELIX record, was skipped: HELIX 33 AD6 PRO111 6 SER111 50 1 45 Bad HELIX record, was skipped: HELIX 34 AD7 PHEDDD 7 GLYDDD 31 1 25 Bad HELIX record, was skipped: HELIX 35 AD8 SERIII 2 SERIII 32 1 31 Bad HELIX record, was skipped: HELIX 36 AD9 PRONNN 6 SERNNN 50 1 45 Bad HELIX record, was skipped: HELIX 37 AE1 ALASSS 7 SERSSS 50 1 44 Bad HELIX record, was skipped: HELIX 38 AE2 PROXXX 6 SERXXX 50 1 45 Bad HELIX record, was skipped: HELIX 39 AE3 PROccc 6 SERccc 50 1 45 Bad HELIX record, was skipped: HELIX 40 AE4 PROhhh 6 SERhhh 50 1 45 Bad HELIX record, was skipped: HELIX 41 AE5 PROmmm 6 SERmmm 50 1 45 Bad HELIX record, was skipped: HELIX 42 AE6 PROrrr 6 SERrrr 50 1 45 Bad HELIX record, was skipped: HELIX 43 AE7 PROwww 6 SERwww 50 1 45 Bad HELIX record, was skipped: HELIX 44 AE8 PROzzz 6 SERzzz 50 1 45 Bad HELIX record, was skipped: HELIX 45 AE9 PHEEEE 7 GLYEEE 31 1 25 Bad HELIX record, was skipped: HELIX 46 AF1 SERJJJ 2 SERJJJ 32 1 31 Bad HELIX record, was skipped: HELIX 47 AF2 PROOOO 6 SEROOO 50 1 45 Bad HELIX record, was skipped: HELIX 48 AF3 ALATTT 7 SERTTT 50 1 44 Bad HELIX record, was skipped: HELIX 49 AF4 PROYYY 6 SERYYY 50 1 45 Bad HELIX record, was skipped: HELIX 50 AF5 PROddd 6 SERddd 50 1 45 Bad HELIX record, was skipped: HELIX 51 AF6 PROiii 6 SERiii 50 1 45 Bad HELIX record, was skipped: HELIX 52 AF7 PROnnn 6 SERnnn 50 1 45 Bad HELIX record, was skipped: HELIX 53 AF8 PROsss 6 SERsss 50 1 45 Bad HELIX record, was skipped: HELIX 54 AF9 PROxxx 6 SERxxx 50 1 45 Bad HELIX record, was skipped: HELIX 55 AG1 PRO333 6 SER333 50 1 45 Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_15832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_15832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_15832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_15832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3p_15832/11_2023/8b3p_15832.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 Residue "FF GLU 29": "OE1" <-> "OE2" Residue "GG GLU 29": "OE1" <-> "OE2" Residue "HH GLU 29": "OE1" <-> "OE2" Residue "II GLU 29": "OE1" <-> "OE2" Residue "JJ GLU 29": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17620 Number of models: 1 Model: "" Number of chains: 55 Chain: "AA" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "FF" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "KK" 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: "PP" 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: "UU" 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: "ZZ" 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: "ee" 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: "jj" 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: "oo" 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: "tt" 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: "yy" 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: "BB" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "GG" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "LL" 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: "QQ" 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: "VV" 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: "aa" 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: "ff" 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: "kk" 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: "pp" 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: "uu" 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: "22" 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: "CC" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "HH" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "MM" 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: "RR" 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: "WW" 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: "bb" 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: "gg" 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: "ll" 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: "qq" 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: "vv" 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: "11" 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: "DD" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "II" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "NN" 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: "SS" 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: "XX" 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: "cc" 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: "hh" 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: "mm" 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: "rr" 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: "ww" 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: "zz" 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: "EE" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "JJ" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "OO" 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: "TT" 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: "YY" 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: "dd" 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: "ii" 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: "nn" 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: "ss" 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: "xx" 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: "33" 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: 9.61, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.3 seconds 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... Bad HELIX record, was skipped: HELIX 1 AA1 ASPAAA 6 GLYAAA 31 1 26 Bad HELIX record, was skipped: HELIX 2 AA2 SERFFF 2 SERFFF 32 1 31 Bad HELIX record, was skipped: HELIX 3 AA3 PROKKK 6 SERKKK 50 1 45 Bad HELIX record, was skipped: HELIX 4 AA4 ALAPPP 7 SERPPP 50 1 44 Bad HELIX record, was skipped: HELIX 5 AA5 PROUUU 6 SERUUU 50 1 45 Bad HELIX record, was skipped: HELIX 6 AA6 PROZZZ 6 SERZZZ 50 1 45 Bad HELIX record, was skipped: HELIX 7 AA7 PROeee 6 SEReee 50 1 45 Bad HELIX record, was skipped: HELIX 8 AA8 PROjjj 6 SERjjj 50 1 45 Bad HELIX record, was skipped: HELIX 9 AA9 PROooo 6 SERooo 50 1 45 Bad HELIX record, was skipped: HELIX 10 AB1 PROttt 6 SERttt 50 1 45 Bad HELIX record, was skipped: HELIX 11 AB2 PROyyy 6 SERyyy 50 1 45 Bad HELIX record, was skipped: HELIX 12 AB3 PHEBBB 7 GLYBBB 31 1 25 Bad HELIX record, was skipped: HELIX 13 AB4 SERGGG 2 SERGGG 32 1 31 Bad HELIX record, was skipped: HELIX 14 AB5 PROLLL 6 SERLLL 50 1 45 Bad HELIX record, was skipped: HELIX 15 AB6 ALAQQQ 7 SERQQQ 50 1 44 Bad HELIX record, was skipped: HELIX 16 AB7 PROVVV 6 SERVVV 50 1 45 Bad HELIX record, was skipped: HELIX 17 AB8 PROaaa 6 SERaaa 50 1 45 Bad HELIX record, was skipped: HELIX 18 AB9 PROfff 6 SERfff 50 1 45 Bad HELIX record, was skipped: HELIX 19 AC1 PROkkk 6 SERkkk 50 1 45 Bad HELIX record, was skipped: HELIX 20 AC2 PROppp 6 SERppp 50 1 45 Bad HELIX record, was skipped: HELIX 21 AC3 PROuuu 6 SERuuu 50 1 45 Bad HELIX record, was skipped: HELIX 22 AC4 PRO222 6 SER222 50 1 45 Bad HELIX record, was skipped: HELIX 23 AC5 PHECCC 7 GLYCCC 31 1 25 Bad HELIX record, was skipped: HELIX 24 AC6 SERHHH 2 SERHHH 32 1 31 Bad HELIX record, was skipped: HELIX 25 AC7 PROMMM 6 SERMMM 50 1 45 Bad HELIX record, was skipped: HELIX 26 AC8 ALARRR 7 SERRRR 50 1 44 Bad HELIX record, was skipped: HELIX 27 AC9 PROWWW 6 SERWWW 50 1 45 Bad HELIX record, was skipped: HELIX 28 AD1 PRObbb 6 SERbbb 50 1 45 Bad HELIX record, was skipped: HELIX 29 AD2 PROggg 6 SERggg 50 1 45 Bad HELIX record, was skipped: HELIX 30 AD3 PROlll 6 SERlll 50 1 45 Bad HELIX record, was skipped: HELIX 31 AD4 PROqqq 6 SERqqq 50 1 45 Bad HELIX record, was skipped: HELIX 32 AD5 PROvvv 6 SERvvv 50 1 45 Bad HELIX record, was skipped: HELIX 33 AD6 PRO111 6 SER111 50 1 45 Bad HELIX record, was skipped: HELIX 34 AD7 PHEDDD 7 GLYDDD 31 1 25 Bad HELIX record, was skipped: HELIX 35 AD8 SERIII 2 SERIII 32 1 31 Bad HELIX record, was skipped: HELIX 36 AD9 PRONNN 6 SERNNN 50 1 45 Bad HELIX record, was skipped: HELIX 37 AE1 ALASSS 7 SERSSS 50 1 44 Bad HELIX record, was skipped: HELIX 38 AE2 PROXXX 6 SERXXX 50 1 45 Bad HELIX record, was skipped: HELIX 39 AE3 PROccc 6 SERccc 50 1 45 Bad HELIX record, was skipped: HELIX 40 AE4 PROhhh 6 SERhhh 50 1 45 Bad HELIX record, was skipped: HELIX 41 AE5 PROmmm 6 SERmmm 50 1 45 Bad HELIX record, was skipped: HELIX 42 AE6 PROrrr 6 SERrrr 50 1 45 Bad HELIX record, was skipped: HELIX 43 AE7 PROwww 6 SERwww 50 1 45 Bad HELIX record, was skipped: HELIX 44 AE8 PROzzz 6 SERzzz 50 1 45 Bad HELIX record, was skipped: HELIX 45 AE9 PHEEEE 7 GLYEEE 31 1 25 Bad HELIX record, was skipped: HELIX 46 AF1 SERJJJ 2 SERJJJ 32 1 31 Bad HELIX record, was skipped: HELIX 47 AF2 PROOOO 6 SEROOO 50 1 45 Bad HELIX record, was skipped: HELIX 48 AF3 ALATTT 7 SERTTT 50 1 44 Bad HELIX record, was skipped: HELIX 49 AF4 PROYYY 6 SERYYY 50 1 45 Bad HELIX record, was skipped: HELIX 50 AF5 PROddd 6 SERddd 50 1 45 Bad HELIX record, was skipped: HELIX 51 AF6 PROiii 6 SERiii 50 1 45 Bad HELIX record, was skipped: HELIX 52 AF7 PROnnn 6 SERnnn 50 1 45 Bad HELIX record, was skipped: HELIX 53 AF8 PROsss 6 SERsss 50 1 45 Bad HELIX record, was skipped: HELIX 54 AF9 PROxxx 6 SERxxx 50 1 45 Bad HELIX record, was skipped: HELIX 55 AG1 PRO333 6 SER333 50 1 45 running ksdssp... Secondary structure from input PDB file: 55 helices and 0 sheets defined 94.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'AA' and resid 7 through 30 Processing helix chain 'FF' and resid 2 through 31 removed outlier: 3.599A pdb=" N GLYFF 14 " --> pdb=" O SERFF 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGFF 18 " --> pdb=" O GLYFF 14 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEFF 21 " --> pdb=" O LEUFF 17 " (cutoff:3.500A) Processing helix chain 'KK' and resid 6 through 49 removed outlier: 3.697A pdb=" N ALAKK 16 " --> pdb=" O ASPKK 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERKK 17 " --> pdb=" O SERKK 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAKK 27 " --> pdb=" O GLYKK 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALKK 31 " --> pdb=" O ALAKK 27 " (cutoff:3.500A) Processing helix chain 'PP' and resid 8 through 49 removed outlier: 3.596A pdb=" N ALAPP 27 " --> pdb=" O GLYPP 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALPP 31 " --> pdb=" O ALAPP 27 " (cutoff:3.500A) Processing helix chain 'UU' and resid 6 through 49 removed outlier: 3.579A pdb=" N ALAUU 10 " --> pdb=" O PROUU 6 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAUU 27 " --> pdb=" O GLYUU 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALUU 31 " --> pdb=" O ALAUU 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERUU 47 " --> pdb=" O LYSUU 43 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 6 through 49 removed outlier: 3.574A pdb=" N ALAZZ 10 " --> pdb=" O PROZZ 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALZZ 31 " --> pdb=" O ALAZZ 27 " (cutoff:3.500A) Processing helix chain 'ee' and resid 6 through 49 removed outlier: 3.587A pdb=" N ALAee 10 " --> pdb=" O PROee 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALee 31 " --> pdb=" O ALAee 27 " (cutoff:3.500A) Processing helix chain 'jj' and resid 6 through 49 removed outlier: 3.595A pdb=" N ALAjj 10 " --> pdb=" O PROjj 6 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALjj 31 " --> pdb=" O ALAjj 27 " (cutoff:3.500A) Processing helix chain 'oo' and resid 6 through 49 removed outlier: 3.593A pdb=" N ALAoo 10 " --> pdb=" O PROoo 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAoo 27 " --> pdb=" O GLYoo 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALoo 31 " --> pdb=" O ALAoo 27 " (cutoff:3.500A) Processing helix chain 'tt' and resid 6 through 49 removed outlier: 3.591A pdb=" N ALAtt 10 " --> pdb=" O PROtt 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAtt 27 " --> pdb=" O GLYtt 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALtt 31 " --> pdb=" O ALAtt 27 " (cutoff:3.500A) Processing helix chain 'yy' and resid 6 through 49 removed outlier: 3.594A pdb=" N ALAyy 10 " --> pdb=" O PROyy 6 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALAyy 27 " --> pdb=" O GLYyy 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALyy 31 " --> pdb=" O ALAyy 27 " (cutoff:3.500A) Processing helix chain 'BB' and resid 7 through 30 Processing helix chain 'GG' and resid 2 through 31 removed outlier: 3.599A pdb=" N GLYGG 14 " --> pdb=" O SERGG 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGGG 18 " --> pdb=" O GLYGG 14 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILEGG 21 " --> pdb=" O LEUGG 17 " (cutoff:3.500A) Processing helix chain 'LL' and resid 6 through 49 removed outlier: 3.697A pdb=" N ALALL 16 " --> pdb=" O ASPLL 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERLL 17 " --> pdb=" O SERLL 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALALL 27 " --> pdb=" O GLYLL 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALLL 31 " --> pdb=" O ALALL 27 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 8 through 49 removed outlier: 3.596A pdb=" N ALAQQ 27 " --> pdb=" O GLYQQ 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALQQ 31 " --> pdb=" O ALAQQ 27 " (cutoff:3.500A) Processing helix chain 'VV' and resid 6 through 49 removed outlier: 3.579A pdb=" N ALAVV 10 " --> pdb=" O PROVV 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAVV 27 " --> pdb=" O GLYVV 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALVV 31 " --> pdb=" O ALAVV 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERVV 47 " --> pdb=" O LYSVV 43 " (cutoff:3.500A) Processing helix chain 'aa' and resid 6 through 49 removed outlier: 3.573A pdb=" N ALAaa 10 " --> pdb=" O PROaa 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALaa 31 " --> pdb=" O ALAaa 27 " (cutoff:3.500A) Processing helix chain 'ff' and resid 6 through 49 removed outlier: 3.588A pdb=" N ALAff 10 " --> pdb=" O PROff 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALff 31 " --> pdb=" O ALAff 27 " (cutoff:3.500A) Processing helix chain 'kk' and resid 6 through 49 removed outlier: 3.594A pdb=" N ALAkk 10 " --> pdb=" O PROkk 6 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VALkk 31 " --> pdb=" O ALAkk 27 " (cutoff:3.500A) Processing helix chain 'pp' and resid 6 through 49 removed outlier: 3.592A pdb=" N ALApp 10 " --> pdb=" O PROpp 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALApp 27 " --> pdb=" O GLYpp 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALpp 31 " --> pdb=" O ALApp 27 " (cutoff:3.500A) Processing helix chain 'uu' and resid 6 through 49 removed outlier: 3.591A pdb=" N ALAuu 10 " --> pdb=" O PROuu 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAuu 27 " --> pdb=" O GLYuu 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALuu 31 " --> pdb=" O ALAuu 27 " (cutoff:3.500A) Processing helix chain '22' and resid 6 through 49 removed outlier: 3.595A pdb=" N ALA22 10 " --> pdb=" O PRO22 6 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA22 27 " --> pdb=" O GLY22 23 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL22 31 " --> pdb=" O ALA22 27 " (cutoff:3.500A) Processing helix chain 'CC' and resid 7 through 30 Processing helix chain 'HH' and resid 2 through 31 removed outlier: 3.599A pdb=" N GLYHH 14 " --> pdb=" O SERHH 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGHH 18 " --> pdb=" O GLYHH 14 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILEHH 21 " --> pdb=" O LEUHH 17 " (cutoff:3.500A) Processing helix chain 'MM' and resid 6 through 49 removed outlier: 3.699A pdb=" N ALAMM 16 " --> pdb=" O ASPMM 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERMM 17 " --> pdb=" O SERMM 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALAMM 27 " --> pdb=" O GLYMM 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALMM 31 " --> pdb=" O ALAMM 27 " (cutoff:3.500A) Processing helix chain 'RR' and resid 8 through 49 removed outlier: 3.596A pdb=" N ALARR 27 " --> pdb=" O GLYRR 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALRR 31 " --> pdb=" O ALARR 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERRR 47 " --> pdb=" O LYSRR 43 " (cutoff:3.500A) Processing helix chain 'WW' and resid 6 through 49 removed outlier: 3.580A pdb=" N ALAWW 10 " --> pdb=" O PROWW 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAWW 27 " --> pdb=" O GLYWW 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALWW 31 " --> pdb=" O ALAWW 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERWW 47 " --> pdb=" O LYSWW 43 " (cutoff:3.500A) Processing helix chain 'bb' and resid 6 through 49 removed outlier: 3.574A pdb=" N ALAbb 10 " --> pdb=" O PRObb 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALbb 31 " --> pdb=" O ALAbb 27 " (cutoff:3.500A) Processing helix chain 'gg' and resid 6 through 49 removed outlier: 3.587A pdb=" N ALAgg 10 " --> pdb=" O PROgg 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALgg 31 " --> pdb=" O ALAgg 27 " (cutoff:3.500A) Processing helix chain 'll' and resid 6 through 49 removed outlier: 3.592A pdb=" N ALAll 10 " --> pdb=" O PROll 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALll 31 " --> pdb=" O ALAll 27 " (cutoff:3.500A) Processing helix chain 'qq' and resid 6 through 49 removed outlier: 3.592A pdb=" N ALAqq 10 " --> pdb=" O PROqq 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAqq 27 " --> pdb=" O GLYqq 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALqq 31 " --> pdb=" O ALAqq 27 " (cutoff:3.500A) Processing helix chain 'vv' and resid 6 through 49 removed outlier: 3.591A pdb=" N ALAvv 10 " --> pdb=" O PROvv 6 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAvv 27 " --> pdb=" O GLYvv 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALvv 31 " --> pdb=" O ALAvv 27 " (cutoff:3.500A) Processing helix chain '11' and resid 6 through 49 removed outlier: 3.594A pdb=" N ALA11 10 " --> pdb=" O PRO11 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA11 27 " --> pdb=" O GLY11 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL11 31 " --> pdb=" O ALA11 27 " (cutoff:3.500A) Processing helix chain 'DD' and resid 7 through 30 Processing helix chain 'II' and resid 2 through 31 removed outlier: 3.599A pdb=" N GLYII 14 " --> pdb=" O SERII 10 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGII 18 " --> pdb=" O GLYII 14 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILEII 21 " --> pdb=" O LEUII 17 " (cutoff:3.500A) Processing helix chain 'NN' and resid 6 through 49 removed outlier: 3.698A pdb=" N ALANN 16 " --> pdb=" O ASPNN 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SERNN 17 " --> pdb=" O SERNN 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALANN 27 " --> pdb=" O GLYNN 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALNN 31 " --> pdb=" O ALANN 27 " (cutoff:3.500A) Processing helix chain 'SS' and resid 8 through 49 removed outlier: 3.597A pdb=" N ALASS 27 " --> pdb=" O GLYSS 23 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALSS 31 " --> pdb=" O ALASS 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SERSS 47 " --> pdb=" O LYSSS 43 " (cutoff:3.500A) Processing helix chain 'XX' and resid 6 through 49 removed outlier: 3.579A pdb=" N ALAXX 10 " --> pdb=" O PROXX 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAXX 27 " --> pdb=" O GLYXX 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALXX 31 " --> pdb=" O ALAXX 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERXX 47 " --> pdb=" O LYSXX 43 " (cutoff:3.500A) Processing helix chain 'cc' and resid 6 through 49 removed outlier: 3.574A pdb=" N ALAcc 10 " --> pdb=" O PROcc 6 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALcc 31 " --> pdb=" O ALAcc 27 " (cutoff:3.500A) Processing helix chain 'hh' and resid 6 through 49 removed outlier: 3.587A pdb=" N ALAhh 10 " --> pdb=" O PROhh 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALhh 31 " --> pdb=" O ALAhh 27 " (cutoff:3.500A) Processing helix chain 'mm' and resid 6 through 49 removed outlier: 3.594A pdb=" N ALAmm 10 " --> pdb=" O PROmm 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALmm 31 " --> pdb=" O ALAmm 27 " (cutoff:3.500A) Processing helix chain 'rr' and resid 6 through 49 removed outlier: 3.592A pdb=" N ALArr 10 " --> pdb=" O PROrr 6 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALArr 27 " --> pdb=" O GLYrr 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALrr 31 " --> pdb=" O ALArr 27 " (cutoff:3.500A) Processing helix chain 'ww' and resid 6 through 49 removed outlier: 3.591A pdb=" N ALAww 10 " --> pdb=" O PROww 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAww 27 " --> pdb=" O GLYww 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALww 31 " --> pdb=" O ALAww 27 " (cutoff:3.500A) Processing helix chain 'zz' and resid 6 through 49 removed outlier: 3.595A pdb=" N ALAzz 10 " --> pdb=" O PROzz 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAzz 27 " --> pdb=" O GLYzz 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALzz 31 " --> pdb=" O ALAzz 27 " (cutoff:3.500A) Processing helix chain 'EE' and resid 7 through 30 Processing helix chain 'JJ' and resid 2 through 31 removed outlier: 3.598A pdb=" N GLYJJ 14 " --> pdb=" O SERJJ 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARGJJ 18 " --> pdb=" O GLYJJ 14 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILEJJ 21 " --> pdb=" O LEUJJ 17 " (cutoff:3.500A) Processing helix chain 'OO' and resid 6 through 49 removed outlier: 3.697A pdb=" N ALAOO 16 " --> pdb=" O ASPOO 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SEROO 17 " --> pdb=" O SEROO 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALAOO 27 " --> pdb=" O GLYOO 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VALOO 31 " --> pdb=" O ALAOO 27 " (cutoff:3.500A) Processing helix chain 'TT' and resid 8 through 49 removed outlier: 3.595A pdb=" N ALATT 27 " --> pdb=" O GLYTT 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALTT 31 " --> pdb=" O ALATT 27 " (cutoff:3.500A) Processing helix chain 'YY' and resid 6 through 49 removed outlier: 3.578A pdb=" N ALAYY 10 " --> pdb=" O PROYY 6 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALAYY 27 " --> pdb=" O GLYYY 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALYY 31 " --> pdb=" O ALAYY 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERYY 47 " --> pdb=" O LYSYY 43 " (cutoff:3.500A) Processing helix chain 'dd' and resid 6 through 49 removed outlier: 3.574A pdb=" N ALAdd 10 " --> pdb=" O PROdd 6 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALdd 31 " --> pdb=" O ALAdd 27 " (cutoff:3.500A) Processing helix chain 'ii' and resid 6 through 49 removed outlier: 3.587A pdb=" N ALAii 10 " --> pdb=" O PROii 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VALii 31 " --> pdb=" O ALAii 27 " (cutoff:3.500A) Processing helix chain 'nn' and resid 6 through 49 removed outlier: 3.594A pdb=" N ALAnn 10 " --> pdb=" O PROnn 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALnn 31 " --> pdb=" O ALAnn 27 " (cutoff:3.500A) Processing helix chain 'ss' and resid 6 through 49 removed outlier: 3.593A pdb=" N ALAss 10 " --> pdb=" O PROss 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAss 27 " --> pdb=" O GLYss 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALss 31 " --> pdb=" O ALAss 27 " (cutoff:3.500A) Processing helix chain 'xx' and resid 6 through 49 removed outlier: 3.591A pdb=" N ALAxx 10 " --> pdb=" O PROxx 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAxx 27 " --> pdb=" O GLYxx 23 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALxx 31 " --> pdb=" O ALAxx 27 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 49 removed outlier: 3.595A pdb=" N ALA33 10 " --> pdb=" O PRO33 6 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA33 27 " --> pdb=" O GLY33 23 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL33 31 " --> pdb=" O ALA33 27 " (cutoff:3.500A) 1878 hydrogen bonds defined for protein. 5634 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: 5.47 Time building geometry restraints manager: 7.74 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 ASPtt 5 " pdb=" CA ASPtt 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 ASPuu 5 " pdb=" CA ASPuu 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 METJJ 1 " pdb=" CA METJJ 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 ASPxx 5 " pdb=" CA ASPxx 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 ASPww 5 " pdb=" CA ASPww 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: 97.31 - 104.73: 236 104.73 - 112.16: 7638 112.16 - 119.59: 7795 119.59 - 127.02: 8351 127.02 - 134.45: 165 Bond angle restraints: 24185 Sorted by residual: angle pdb=" C SERHH 19 " pdb=" N GLYHH 20 " pdb=" CA GLYHH 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 SERJJ 19 " pdb=" N GLYJJ 20 " pdb=" CA GLYJJ 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 SERGG 19 " pdb=" N GLYGG 20 " pdb=" CA GLYGG 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 SERFF 19 " pdb=" N GLYFF 20 " pdb=" CA GLYFF 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 SERII 19 " pdb=" N GLYII 20 " pdb=" CA GLYII 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 ASPaa 5 " pdb=" N ASPaa 5 " pdb=" CA ASPaa 5 " pdb=" CB ASPaa 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 ASPdd 5 " pdb=" N ASPdd 5 " pdb=" CA ASPdd 5 " pdb=" CB ASPdd 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 ASPii 5 " pdb=" N ASPii 5 " pdb=" CA ASPii 5 " pdb=" CB ASPii 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 SERYY 50 " pdb=" N SERYY 50 " pdb=" C SERYY 50 " pdb=" CB SERYY 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 SERWW 50 " pdb=" N SERWW 50 " pdb=" C SERWW 50 " pdb=" CB SERWW 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 SERVV 50 " pdb=" N SERVV 50 " pdb=" C SERVV 50 " pdb=" CB SERVV 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 PHESS 11 " -0.025 2.00e-02 2.50e+03 1.66e-02 4.80e+00 pdb=" CG PHESS 11 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHESS 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHESS 11 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHESS 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHESS 11 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHESS 11 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHETT 11 " 0.024 2.00e-02 2.50e+03 1.64e-02 4.73e+00 pdb=" CG PHETT 11 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHETT 11 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHETT 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHETT 11 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHETT 11 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHETT 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHERR 11 " -0.024 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHERR 11 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHERR 11 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHERR 11 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHERR 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHERR 11 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHERR 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: 19576 3.44 - 3.93: 28301 3.93 - 4.41: 29800 4.41 - 4.90: 50187 Nonbonded interactions: 135199 Sorted by model distance: nonbonded pdb=" NE2 GLNQQ 15 " pdb=" SD METMM 28 " model vdw 2.469 2.880 nonbonded pdb=" NE2 GLNPP 15 " pdb=" SD METLL 28 " model vdw 2.482 2.880 nonbonded pdb=" NE2 GLNRR 15 " pdb=" SD METNN 28 " model vdw 2.486 2.880 nonbonded pdb=" SD METKK 28 " pdb=" NE2 GLNTT 15 " model vdw 2.499 2.880 nonbonded pdb=" NE2 GLNSS 15 " pdb=" SD METOO 28 " model vdw 2.504 2.880 ... (remaining 135194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '11' 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 '22' 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 '33' 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 'KK' selection = chain 'LL' selection = chain 'MM' selection = chain 'NN' selection = chain 'OO' selection = chain 'PP' selection = chain 'QQ' selection = chain 'RR' selection = chain 'SS' selection = chain 'TT' selection = chain 'UU' selection = chain 'VV' selection = chain 'WW' selection = chain 'XX' selection = chain 'YY' selection = (chain 'ZZ' 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 'aa' 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 'bb' 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 'cc' 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 'dd' 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 'ee' 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 'ff' 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 'gg' 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 'hh' 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 'ii' 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 'jj' 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 'kk' 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 'll' 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 'mm' 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 'nn' 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 'oo' 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 'pp' 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 'qq' 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 'rr' 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 'ss' 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 'tt' 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 'uu' 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 'vv' 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 'ww' 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 'xx' 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 'yy' 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 'zz' 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 'AA' selection = chain 'BB' selection = chain 'CC' selection = chain 'DD' selection = chain 'EE' } ncs_group { reference = chain 'FF' selection = chain 'GG' selection = chain 'HH' selection = chain 'II' selection = chain 'JJ' } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.340 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 47.310 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.110 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 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= 0.501 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 2260 helix: -0.36 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.01 (0.05), residues: 45 *********************** 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 fitting. rotamer outliers: 14 poor density : 608 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 613 average time/residue: 1.5551 time to fit residues: 1042.7255 Evaluate side-chains 382 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2834 time to fit residues: 4.2516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 186 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 32 GLN PP 15 GLN oo 15 GLN BB 32 GLN QQ 15 GLN pp 15 GLN CC 32 GLN qq 15 GLN DD 32 GLN SS 15 GLN rr 15 GLN zz 15 GLN EE 12 GLN EE 32 GLN TT 15 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17930 Z= 0.197 Angle : 0.485 5.522 24185 Z= 0.276 Chirality : 0.034 0.136 2900 Planarity : 0.003 0.018 2885 Dihedral : 7.450 70.915 2420 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.61 % Allowed : 23.42 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.15), residues: 2260 helix: 2.93 (0.09), residues: 2175 sheet: None (None), residues: 0 loop : -4.46 (0.36), residues: 85 *********************** 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 609 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 491 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 21 residues processed: 538 average time/residue: 1.2882 time to fit residues: 768.8779 Evaluate side-chains 362 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 341 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.4550 time to fit residues: 8.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: oo 15 GLN QQ 15 GLN DD 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17930 Z= 0.300 Angle : 0.502 6.324 24185 Z= 0.281 Chirality : 0.034 0.113 2900 Planarity : 0.003 0.016 2885 Dihedral : 6.003 62.987 2420 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.32 % Allowed : 28.18 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.93 (0.15), residues: 2260 helix: 3.34 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -5.62 (0.56), residues: 45 *********************** 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 472 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 377 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 42 residues processed: 420 average time/residue: 1.4773 time to fit residues: 682.4272 Evaluate side-chains 380 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 25 residues processed: 17 average time/residue: 0.7576 time to fit residues: 17.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 12 GLN ** TT 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17930 Z= 0.190 Angle : 0.458 7.811 24185 Z= 0.249 Chirality : 0.032 0.119 2900 Planarity : 0.002 0.019 2885 Dihedral : 5.323 48.766 2420 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.09 % Allowed : 28.18 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.62 (0.15), residues: 2260 helix: 3.78 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -5.63 (0.58), residues: 45 *********************** 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 461 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 388 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 32 residues processed: 420 average time/residue: 1.4690 time to fit residues: 678.7044 Evaluate side-chains 361 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 11 average time/residue: 0.6839 time to fit residues: 11.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 50 optimal weight: 0.0040 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** QQ 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RR 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EE 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17930 Z= 0.221 Angle : 0.478 8.283 24185 Z= 0.260 Chirality : 0.032 0.112 2900 Planarity : 0.002 0.019 2885 Dihedral : 5.151 48.364 2420 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 29.97 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.69 (0.15), residues: 2260 helix: 3.81 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -5.10 (0.60), residues: 45 *********************** 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 431 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 361 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 393 average time/residue: 1.4719 time to fit residues: 636.2177 Evaluate side-chains 364 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.8326 time to fit residues: 8.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 0.0030 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SS 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17930 Z= 0.188 Angle : 0.472 7.114 24185 Z= 0.256 Chirality : 0.032 0.121 2900 Planarity : 0.002 0.022 2885 Dihedral : 5.097 47.058 2420 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.59 % Allowed : 29.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.88 (0.15), residues: 2260 helix: 3.93 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.82 (0.61), residues: 45 *********************** 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 440 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 376 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 29 residues processed: 410 average time/residue: 1.4430 time to fit residues: 652.9558 Evaluate side-chains 369 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 340 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 20 residues processed: 9 average time/residue: 0.7134 time to fit residues: 10.2741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SS 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17930 Z= 0.209 Angle : 0.501 8.940 24185 Z= 0.271 Chirality : 0.033 0.261 2900 Planarity : 0.003 0.025 2885 Dihedral : 5.067 46.603 2420 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.91 % Allowed : 31.99 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.75 (0.16), residues: 2260 helix: 3.84 (0.09), residues: 2215 sheet: None (None), residues: 0 loop : -4.66 (0.60), residues: 45 *********************** 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 400 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 348 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 26 residues processed: 377 average time/residue: 1.4823 time to fit residues: 614.3921 Evaluate side-chains 363 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 337 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.5409 time to fit residues: 6.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17930 Z= 0.192 Angle : 0.498 8.890 24185 Z= 0.271 Chirality : 0.033 0.210 2900 Planarity : 0.003 0.025 2885 Dihedral : 5.035 46.205 2420 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.69 % Allowed : 32.38 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.77 (0.16), residues: 2260 helix: 3.86 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -4.64 (0.60), residues: 45 *********************** 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 411 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 390 average time/residue: 1.5089 time to fit residues: 650.1172 Evaluate side-chains 363 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 341 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.6850 time to fit residues: 4.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17930 Z= 0.230 Angle : 0.536 10.824 24185 Z= 0.292 Chirality : 0.034 0.170 2900 Planarity : 0.003 0.030 2885 Dihedral : 5.020 45.893 2420 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.18 % Allowed : 33.17 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.16), residues: 2260 helix: 3.70 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -4.59 (0.59), residues: 45 *********************** 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 384 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 345 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 372 average time/residue: 1.5940 time to fit residues: 650.4888 Evaluate side-chains 363 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 339 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.5373 time to fit residues: 4.4785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17930 Z= 0.242 Angle : 0.550 10.696 24185 Z= 0.303 Chirality : 0.034 0.180 2900 Planarity : 0.003 0.033 2885 Dihedral : 4.996 45.780 2420 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.79 % Allowed : 33.67 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.38 (0.16), residues: 2260 helix: 3.61 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -4.63 (0.59), residues: 45 ********************** 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 371 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 339 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 363 average time/residue: 1.4953 time to fit residues: 596.1432 Evaluate side-chains 356 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 335 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.4570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 22 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052237 restraints weight = 53575.405| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.58 r_work: 0.2958 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.5635 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= 0.195 Angle : 0.548 11.649 24185 Z= 0.296 Chirality : 0.033 0.197 2900 Planarity : 0.003 0.034 2885 Dihedral : 5.055 45.946 2420 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 33.39 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.16), residues: 2260 helix: 3.77 (0.10), residues: 2215 sheet: None (None), residues: 0 loop : -4.56 (0.61), residues: 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9088.60 seconds wall clock time: 162 minutes 34.50 seconds (9754.50 seconds total)