Starting phenix.real_space_refine on Wed Apr 30 21:34:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.map" model { file = "/net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j63_5830/04_2025/3j63_5830.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 60 5.16 5 C 6675 2.51 5 N 1830 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "O" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Residues with excluded nonbonded symmetry interactions: 1365 residue: pdb=" N MET A 1 " occ=0.44 ... (6 atoms not shown) pdb=" CE MET A 1 " occ=0.44 residue: pdb=" N GLY A 2 " occ=0.41 ... (2 atoms not shown) pdb=" O GLY A 2 " occ=0.41 residue: pdb=" N ARG A 3 " occ=0.57 ... (9 atoms not shown) pdb=" NH2 ARG A 3 " occ=0.57 residue: pdb=" N ALA A 4 " occ=0.58 ... (3 atoms not shown) pdb=" CB ALA A 4 " occ=0.58 residue: pdb=" N ARG A 5 " occ=0.78 ... (9 atoms not shown) pdb=" NH2 ARG A 5 " occ=0.78 residue: pdb=" N ASP A 6 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 6 " occ=0.60 residue: pdb=" N ALA A 7 " occ=0.49 ... (3 atoms not shown) pdb=" CB ALA A 7 " occ=0.49 residue: pdb=" N ILE A 8 " occ=0.71 ... (6 atoms not shown) pdb=" CD1 ILE A 8 " occ=0.71 residue: pdb=" N LEU A 9 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 9 " occ=0.80 residue: pdb=" N ASP A 10 " occ=0.58 ... (6 atoms not shown) pdb=" OD2 ASP A 10 " occ=0.58 residue: pdb=" N ALA A 11 " occ=0.51 ... (3 atoms not shown) pdb=" CB ALA A 11 " occ=0.51 residue: pdb=" N LEU A 12 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 12 " occ=0.80 ... (remaining 1353 not shown) Time building chain proxies: 6.28, per 1000 atoms: 0.59 Number of scatterers: 10590 At special positions: 0 Unit cell: (93.96, 96.12, 99.36, 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 60 16.00 O 2025 8.00 N 1830 7.00 C 6675 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: 3.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.828A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.843A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.667A pdb=" N LEU A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.764A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.231A pdb=" N GLY A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.702A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.890A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.589A pdb=" N LEU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.712A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 4.268A pdb=" N GLY B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 removed outlier: 3.547A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.881A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.565A pdb=" N LEU C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.689A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 4.203A pdb=" N GLY C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 9 Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.839A pdb=" N LYS D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.692A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.890A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.782A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.611A pdb=" N GLN D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 removed outlier: 4.106A pdb=" N ASP E 6 " --> pdb=" O GLY E 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.902A pdb=" N LYS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.019A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.663A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 91 removed outlier: 4.218A pdb=" N GLY E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.727A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.519A pdb=" N LEU F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 47 removed outlier: 3.615A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 60 removed outlier: 4.056A pdb=" N LEU F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.856A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 removed outlier: 4.249A pdb=" N GLY F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 4 Processing helix chain 'G' and resid 5 through 10 Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 47 removed outlier: 3.672A pdb=" N LEU G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.802A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.539A pdb=" N GLN G 84 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 removed outlier: 3.705A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 30 removed outlier: 3.943A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 3.568A pdb=" N LEU H 44 " --> pdb=" O PRO H 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 removed outlier: 3.836A pdb=" N LEU H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 76 removed outlier: 3.808A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.636A pdb=" N GLN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.666A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 47 removed outlier: 3.697A pdb=" N LEU I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 60 removed outlier: 4.049A pdb=" N LEU I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.806A pdb=" N GLU I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 removed outlier: 4.366A pdb=" N GLY I 83 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN I 84 " --> pdb=" O GLU I 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 88 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 10 removed outlier: 3.527A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.951A pdb=" N LYS J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.671A pdb=" N LEU J 44 " --> pdb=" O PRO J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 removed outlier: 3.819A pdb=" N LEU J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.763A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 91 removed outlier: 4.227A pdb=" N GLY J 83 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 88 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.959A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.803A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.633A pdb=" N LEU K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 60 removed outlier: 3.883A pdb=" N LEU K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 76 removed outlier: 3.787A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 removed outlier: 4.148A pdb=" N GLY K 83 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN K 84 " --> pdb=" O GLU K 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.853A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.901A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 47 removed outlier: 3.604A pdb=" N LEU L 44 " --> pdb=" O PRO L 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 60 removed outlier: 3.844A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 76 removed outlier: 3.646A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 91 removed outlier: 4.254A pdb=" N GLY L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN L 86 " --> pdb=" O ALA L 82 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 88 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.849A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.008A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU M 28 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 removed outlier: 3.511A pdb=" N LEU M 44 " --> pdb=" O PRO M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 76 removed outlier: 3.755A pdb=" N GLU M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.514A pdb=" N GLN M 84 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA M 88 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 10 removed outlier: 4.074A pdb=" N ASP N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.940A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 76 removed outlier: 3.630A pdb=" N GLU N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 4.295A pdb=" N GLY N 83 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.701A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.002A pdb=" N LYS O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU O 28 " --> pdb=" O LYS O 24 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER O 29 " --> pdb=" O LEU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 47 removed outlier: 3.783A pdb=" N LEU O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 removed outlier: 4.018A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.819A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.630A pdb=" N GLN O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA O 88 " --> pdb=" O GLN O 84 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1404 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: 2.59 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3570 1.34 - 1.46: 1003 1.46 - 1.57: 6002 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 10695 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 10690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12919 1.86 - 3.72: 1257 3.72 - 5.58: 140 5.58 - 7.44: 56 7.44 - 9.30: 13 Bond angle restraints: 14385 Sorted by residual: angle pdb=" N SER G 29 " pdb=" CA SER G 29 " pdb=" C SER G 29 " ideal model delta sigma weight residual 111.28 119.35 -8.07 1.09e+00 8.42e-01 5.49e+01 angle pdb=" N VAL D 30 " pdb=" CA VAL D 30 " pdb=" C VAL D 30 " ideal model delta sigma weight residual 108.96 117.07 -8.11 1.10e+00 8.26e-01 5.44e+01 angle pdb=" N VAL B 30 " pdb=" CA VAL B 30 " pdb=" C VAL B 30 " ideal model delta sigma weight residual 108.96 116.99 -8.03 1.10e+00 8.26e-01 5.33e+01 angle pdb=" N VAL E 30 " pdb=" CA VAL E 30 " pdb=" C VAL E 30 " ideal model delta sigma weight residual 108.96 116.73 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" N VAL M 30 " pdb=" CA VAL M 30 " pdb=" C VAL M 30 " ideal model delta sigma weight residual 108.96 116.41 -7.45 1.10e+00 8.26e-01 4.59e+01 ... (remaining 14380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5853 17.23 - 34.46: 487 34.46 - 51.69: 136 51.69 - 68.92: 140 68.92 - 86.15: 14 Dihedral angle restraints: 6630 sinusoidal: 2715 harmonic: 3915 Sorted by residual: dihedral pdb=" CB GLU L 80 " pdb=" CG GLU L 80 " pdb=" CD GLU L 80 " pdb=" OE1 GLU L 80 " ideal model delta sinusoidal sigma weight residual 0.00 86.15 -86.15 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" N LEU D 61 " pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sinusoidal sigma weight residual -180.00 -120.71 -59.29 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET O 1 " pdb=" CG MET O 1 " pdb=" SD MET O 1 " pdb=" CE MET O 1 " ideal model delta sinusoidal sigma weight residual -180.00 -120.73 -59.27 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 729 0.045 - 0.090: 595 0.090 - 0.135: 264 0.135 - 0.179: 78 0.179 - 0.224: 14 Chirality restraints: 1680 Sorted by residual: chirality pdb=" CA SER C 29 " pdb=" N SER C 29 " pdb=" C SER C 29 " pdb=" CB SER C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA SER L 29 " pdb=" N SER L 29 " pdb=" C SER L 29 " pdb=" CB SER L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA SER G 29 " pdb=" N SER G 29 " pdb=" C SER G 29 " pdb=" CB SER G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1677 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 36 " 0.028 2.00e-02 2.50e+03 1.41e-02 3.98e+00 pdb=" CG TYR O 36 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 36 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR O 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 30 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO O 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO O 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO O 31 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 30 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO M 31 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 31 " 0.023 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 979 2.73 - 3.27: 12830 3.27 - 3.81: 17234 3.81 - 4.36: 20542 4.36 - 4.90: 31132 Nonbonded interactions: 82717 Sorted by model distance: nonbonded pdb=" O VAL M 57 " pdb=" O TYR M 60 " model vdw 2.184 3.040 nonbonded pdb=" O LEU M 50 " pdb=" OG1 THR M 53 " model vdw 2.281 3.040 nonbonded pdb=" O LEU H 50 " pdb=" OG1 THR H 53 " model vdw 2.286 3.040 nonbonded pdb=" O LEU A 50 " pdb=" OG1 THR A 53 " model vdw 2.290 3.040 nonbonded pdb=" O LEU J 50 " pdb=" OG1 THR J 53 " model vdw 2.293 3.040 ... (remaining 82712 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.30 max=0.99 mean=0.64 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 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: 0.350 Check model and map are aligned: 0.000 Set scattering table: 0.090 Process input model: 26.180 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 0.005 0.033 10695 Z= 0.300 Angle : 1.252 9.305 14385 Z= 0.876 Chirality : 0.072 0.224 1680 Planarity : 0.004 0.042 1860 Dihedral : 17.395 86.154 4110 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 54.83 Ramachandran Plot: Outliers : 3.07 % Allowed : 10.26 % Favored : 86.67 % Rotamer: Outliers : 7.31 % Allowed : 15.25 % Favored : 77.44 % 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: -4.14 (0.19), residues: 1335 helix: -4.38 (0.12), residues: 510 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 90 PHE 0.008 0.002 PHE B 23 TYR 0.028 0.004 TYR O 36 ARG 0.006 0.001 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.33265 ( 475) hydrogen bonds : angle 10.76444 ( 1404) covalent geometry : bond 0.00457 (10695) covalent geometry : angle 1.25221 (14385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 519 time to evaluate : 1.080 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: A 1 MET cc_start: 0.5777 (mtm) cc_final: 0.5392 (ttt) REVERT: A 85 LEU cc_start: 0.6904 (tp) cc_final: 0.6538 (tp) REVERT: B 1 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4407 (ttt) REVERT: B 12 LEU cc_start: 0.6904 (mm) cc_final: 0.6435 (mm) REVERT: B 50 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6925 (mt) REVERT: C 1 MET cc_start: 0.5610 (mtm) cc_final: 0.4611 (ttp) REVERT: C 51 ASP cc_start: 0.6024 (m-30) cc_final: 0.5677 (m-30) REVERT: D 1 MET cc_start: 0.5761 (mtm) cc_final: 0.4999 (ttt) REVERT: D 50 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7522 (mt) REVERT: F 1 MET cc_start: 0.5443 (mtm) cc_final: 0.4991 (ttt) REVERT: F 50 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6691 (mt) REVERT: I 1 MET cc_start: 0.6093 (mtm) cc_final: 0.4462 (ttt) REVERT: J 1 MET cc_start: 0.6505 (mtm) cc_final: 0.4544 (ttt) REVERT: J 51 ASP cc_start: 0.5744 (m-30) cc_final: 0.5136 (m-30) REVERT: K 1 MET cc_start: 0.5903 (mtt) cc_final: 0.5185 (ttm) REVERT: K 34 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: K 51 ASP cc_start: 0.5821 (m-30) cc_final: 0.5243 (m-30) REVERT: K 85 LEU cc_start: 0.6151 (tp) cc_final: 0.5909 (tp) REVERT: M 50 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6889 (mt) REVERT: N 12 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6157 (mm) REVERT: N 50 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7408 (mt) REVERT: N 51 ASP cc_start: 0.5731 (m-30) cc_final: 0.5207 (m-30) REVERT: N 85 LEU cc_start: 0.6346 (tp) cc_final: 0.6046 (tp) REVERT: O 1 MET cc_start: 0.6501 (mtt) cc_final: 0.5412 (ttt) REVERT: O 34 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: O 47 MET cc_start: 0.7473 (mmt) cc_final: 0.7237 (mmt) REVERT: O 51 ASP cc_start: 0.5588 (m-30) cc_final: 0.4977 (m-30) outliers start: 80 outliers final: 36 residues processed: 556 average time/residue: 0.2368 time to fit residues: 179.7262 Evaluate side-chains 407 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain O residue 34 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 14 ASN E 14 ASN F 14 ASN G 14 ASN G 71 ASN J 14 ASN K 14 ASN L 14 ASN N 14 ASN O 14 ASN O 90 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110188 restraints weight = 34032.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112154 restraints weight = 15842.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113439 restraints weight = 8833.684| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 0.99 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10695 Z= 0.179 Angle : 0.878 10.102 14385 Z= 0.429 Chirality : 0.041 0.189 1680 Planarity : 0.006 0.071 1860 Dihedral : 9.159 58.334 1595 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.76 % Allowed : 28.22 % Favored : 65.02 % 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: -2.58 (0.21), residues: 1335 helix: -2.17 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.46 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 90 PHE 0.029 0.003 PHE B 59 TYR 0.022 0.002 TYR G 64 ARG 0.004 0.001 ARG E 41 Details of bonding type rmsd hydrogen bonds : bond 0.06345 ( 475) hydrogen bonds : angle 6.85839 ( 1404) covalent geometry : bond 0.00364 (10695) covalent geometry : angle 0.87825 (14385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 1.134 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: A 1 MET cc_start: 0.6688 (mtm) cc_final: 0.6407 (ttt) REVERT: B 1 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.5687 (ttt) REVERT: C 1 MET cc_start: 0.7140 (mtm) cc_final: 0.6005 (ttp) REVERT: C 26 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8169 (ttpp) REVERT: C 39 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8324 (mt) REVERT: D 1 MET cc_start: 0.7427 (mtm) cc_final: 0.6076 (ttt) REVERT: D 9 LEU cc_start: 0.8680 (tp) cc_final: 0.8436 (tp) REVERT: D 10 ASP cc_start: 0.8488 (m-30) cc_final: 0.8216 (t0) REVERT: D 50 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8098 (mt) REVERT: E 8 ILE cc_start: 0.8533 (mm) cc_final: 0.8176 (tp) REVERT: F 1 MET cc_start: 0.7345 (mtm) cc_final: 0.6029 (ttt) REVERT: F 51 ASP cc_start: 0.8343 (m-30) cc_final: 0.8032 (m-30) REVERT: F 58 SER cc_start: 0.8672 (m) cc_final: 0.8295 (p) REVERT: H 8 ILE cc_start: 0.9162 (mm) cc_final: 0.8879 (tp) REVERT: H 38 ARG cc_start: 0.6640 (mtt180) cc_final: 0.6345 (mtt180) REVERT: H 73 LEU cc_start: 0.8664 (mt) cc_final: 0.8077 (tp) REVERT: I 1 MET cc_start: 0.7467 (mtt) cc_final: 0.5427 (ttt) REVERT: I 67 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6812 (mm-30) REVERT: J 1 MET cc_start: 0.7691 (mtm) cc_final: 0.5515 (ttt) REVERT: J 51 ASP cc_start: 0.7090 (m-30) cc_final: 0.6884 (m-30) REVERT: J 79 GLN cc_start: 0.6120 (mp10) cc_final: 0.5840 (mp10) REVERT: K 1 MET cc_start: 0.7451 (mtt) cc_final: 0.6261 (ttm) REVERT: K 5 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7416 (ptm160) REVERT: K 51 ASP cc_start: 0.7902 (m-30) cc_final: 0.7436 (m-30) REVERT: L 50 LEU cc_start: 0.8395 (mt) cc_final: 0.8167 (mt) REVERT: M 6 ASP cc_start: 0.8471 (t70) cc_final: 0.8252 (t0) REVERT: M 51 ASP cc_start: 0.8661 (m-30) cc_final: 0.8336 (m-30) REVERT: O 1 MET cc_start: 0.7845 (mtt) cc_final: 0.6519 (ttt) REVERT: O 8 ILE cc_start: 0.9182 (mm) cc_final: 0.8703 (tp) REVERT: O 24 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8652 (mtpp) REVERT: O 26 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8079 (ttpt) REVERT: O 51 ASP cc_start: 0.7612 (m-30) cc_final: 0.6824 (m-30) outliers start: 74 outliers final: 42 residues processed: 479 average time/residue: 0.2594 time to fit residues: 166.4287 Evaluate side-chains 420 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 374 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 40.0000 chunk 133 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094272 restraints weight = 39069.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096111 restraints weight = 15360.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097275 restraints weight = 7723.164| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10695 Z= 0.161 Angle : 0.797 7.004 14385 Z= 0.382 Chirality : 0.040 0.268 1680 Planarity : 0.005 0.058 1860 Dihedral : 7.578 58.499 1525 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 10.87 % Allowed : 28.22 % Favored : 60.91 % 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: -1.45 (0.22), residues: 1335 helix: -1.43 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.25 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.011 0.002 PHE B 59 TYR 0.015 0.002 TYR O 64 ARG 0.003 0.000 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 475) hydrogen bonds : angle 6.18016 ( 1404) covalent geometry : bond 0.00341 (10695) covalent geometry : angle 0.79660 (14385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 400 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7142 (mtm) cc_final: 0.6520 (ttt) REVERT: B 26 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8440 (ttpt) REVERT: C 1 MET cc_start: 0.6352 (mtm) cc_final: 0.5733 (mtp) REVERT: C 26 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8460 (ttpt) REVERT: D 1 MET cc_start: 0.7399 (mtm) cc_final: 0.5898 (ttt) REVERT: D 10 ASP cc_start: 0.8787 (m-30) cc_final: 0.8383 (t0) REVERT: E 8 ILE cc_start: 0.8712 (mm) cc_final: 0.8401 (tp) REVERT: E 76 MET cc_start: 0.5323 (ttt) cc_final: 0.4878 (ttp) REVERT: F 1 MET cc_start: 0.6843 (mtm) cc_final: 0.5930 (ttt) REVERT: F 8 ILE cc_start: 0.8947 (mm) cc_final: 0.8555 (tp) REVERT: F 20 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8224 (tm) REVERT: F 51 ASP cc_start: 0.7871 (m-30) cc_final: 0.7439 (m-30) REVERT: I 1 MET cc_start: 0.7303 (mtt) cc_final: 0.5718 (ttt) REVERT: I 39 ILE cc_start: 0.9108 (mp) cc_final: 0.8727 (mm) REVERT: I 67 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6755 (mm-30) REVERT: J 1 MET cc_start: 0.7725 (mtm) cc_final: 0.5468 (ttt) REVERT: J 79 GLN cc_start: 0.6090 (mp10) cc_final: 0.5846 (mp10) REVERT: K 1 MET cc_start: 0.7452 (mtt) cc_final: 0.6125 (ttm) REVERT: K 5 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7412 (ptm160) REVERT: K 51 ASP cc_start: 0.8099 (m-30) cc_final: 0.7882 (m-30) REVERT: L 73 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8449 (mt) REVERT: M 39 ILE cc_start: 0.8805 (mp) cc_final: 0.8512 (mm) REVERT: O 1 MET cc_start: 0.7532 (mtt) cc_final: 0.6048 (ttt) REVERT: O 8 ILE cc_start: 0.9193 (mm) cc_final: 0.8789 (tp) REVERT: O 26 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8067 (ttpt) REVERT: O 51 ASP cc_start: 0.8286 (m-30) cc_final: 0.7865 (m-30) outliers start: 119 outliers final: 86 residues processed: 465 average time/residue: 0.2412 time to fit residues: 151.5999 Evaluate side-chains 457 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 367 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 26 LYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 0.0370 chunk 91 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088443 restraints weight = 38560.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090106 restraints weight = 14317.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091139 restraints weight = 6811.641| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10695 Z= 0.147 Angle : 0.738 7.216 14385 Z= 0.353 Chirality : 0.038 0.163 1680 Planarity : 0.005 0.060 1860 Dihedral : 7.304 58.761 1522 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 12.69 % Allowed : 29.13 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1335 helix: -1.19 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.13 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 90 PHE 0.009 0.002 PHE A 59 TYR 0.013 0.002 TYR J 64 ARG 0.006 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 475) hydrogen bonds : angle 5.78381 ( 1404) covalent geometry : bond 0.00317 (10695) covalent geometry : angle 0.73779 (14385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 405 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6903 (mtm) cc_final: 0.6280 (ttt) REVERT: A 8 ILE cc_start: 0.8886 (mm) cc_final: 0.8251 (tp) REVERT: B 20 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8708 (tm) REVERT: C 1 MET cc_start: 0.6371 (mtm) cc_final: 0.5651 (mtp) REVERT: C 51 ASP cc_start: 0.8881 (m-30) cc_final: 0.8679 (m-30) REVERT: D 1 MET cc_start: 0.7669 (mtm) cc_final: 0.5939 (ttt) REVERT: D 10 ASP cc_start: 0.8898 (m-30) cc_final: 0.8397 (t0) REVERT: E 8 ILE cc_start: 0.8568 (mm) cc_final: 0.8302 (tp) REVERT: F 1 MET cc_start: 0.7061 (mtm) cc_final: 0.6204 (ttt) REVERT: F 8 ILE cc_start: 0.8906 (mm) cc_final: 0.8512 (tp) REVERT: F 20 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8384 (tm) REVERT: F 51 ASP cc_start: 0.7801 (m-30) cc_final: 0.7271 (m-30) REVERT: G 26 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8278 (ttpt) REVERT: G 59 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8264 (t80) REVERT: H 81 MET cc_start: 0.7635 (ppp) cc_final: 0.6939 (ppp) REVERT: I 1 MET cc_start: 0.7310 (mtt) cc_final: 0.5861 (ttt) REVERT: I 67 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6678 (mm-30) REVERT: J 1 MET cc_start: 0.7483 (mtm) cc_final: 0.5534 (ttt) REVERT: K 1 MET cc_start: 0.6995 (mtt) cc_final: 0.6160 (ttt) REVERT: K 5 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: K 50 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8188 (mt) REVERT: K 75 ASP cc_start: 0.7225 (m-30) cc_final: 0.6806 (m-30) REVERT: L 25 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8780 (tt) REVERT: L 81 MET cc_start: 0.7640 (ppp) cc_final: 0.7258 (ppp) REVERT: M 26 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8328 (ttpt) REVERT: O 1 MET cc_start: 0.7452 (mtt) cc_final: 0.6066 (ttt) REVERT: O 8 ILE cc_start: 0.9187 (mm) cc_final: 0.8811 (tp) REVERT: O 20 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8138 (tm) REVERT: O 26 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8030 (ttpt) REVERT: O 51 ASP cc_start: 0.8143 (m-30) cc_final: 0.7753 (m-30) outliers start: 139 outliers final: 91 residues processed: 488 average time/residue: 0.2420 time to fit residues: 160.6581 Evaluate side-chains 468 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 369 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 LYS Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085774 restraints weight = 38544.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087361 restraints weight = 13350.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088309 restraints weight = 6170.344| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10695 Z= 0.176 Angle : 0.787 8.222 14385 Z= 0.373 Chirality : 0.040 0.174 1680 Planarity : 0.005 0.053 1860 Dihedral : 7.038 56.786 1516 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 13.52 % Allowed : 29.04 % Favored : 57.44 % 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: -0.88 (0.23), residues: 1335 helix: -1.29 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.39 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 90 PHE 0.011 0.002 PHE O 59 TYR 0.016 0.002 TYR J 64 ARG 0.005 0.000 ARG N 5 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 475) hydrogen bonds : angle 5.78677 ( 1404) covalent geometry : bond 0.00372 (10695) covalent geometry : angle 0.78670 (14385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 395 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6965 (mtm) cc_final: 0.6213 (ttt) REVERT: A 8 ILE cc_start: 0.8706 (mm) cc_final: 0.7994 (tp) REVERT: B 20 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8792 (tm) REVERT: C 1 MET cc_start: 0.6374 (mtm) cc_final: 0.5596 (mtp) REVERT: C 51 ASP cc_start: 0.8969 (m-30) cc_final: 0.8651 (m-30) REVERT: D 1 MET cc_start: 0.7089 (mtm) cc_final: 0.6162 (ttt) REVERT: D 10 ASP cc_start: 0.8858 (m-30) cc_final: 0.8437 (t0) REVERT: E 8 ILE cc_start: 0.8520 (mm) cc_final: 0.8270 (tp) REVERT: F 1 MET cc_start: 0.7089 (mtm) cc_final: 0.6005 (ttt) REVERT: F 8 ILE cc_start: 0.8871 (mm) cc_final: 0.8462 (tp) REVERT: F 51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7617 (m-30) REVERT: F 81 MET cc_start: 0.8288 (tmm) cc_final: 0.7691 (ppp) REVERT: G 8 ILE cc_start: 0.8910 (mm) cc_final: 0.8584 (tp) REVERT: G 26 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8419 (ttpt) REVERT: G 39 ILE cc_start: 0.8824 (mp) cc_final: 0.8529 (mm) REVERT: G 59 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8246 (t80) REVERT: H 81 MET cc_start: 0.7544 (ppp) cc_final: 0.7010 (ppp) REVERT: I 1 MET cc_start: 0.7110 (mtt) cc_final: 0.5939 (ttt) REVERT: I 67 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6829 (mm-30) REVERT: J 1 MET cc_start: 0.7204 (mtm) cc_final: 0.5340 (ttt) REVERT: J 51 ASP cc_start: 0.7779 (m-30) cc_final: 0.7449 (m-30) REVERT: K 1 MET cc_start: 0.7329 (mtt) cc_final: 0.6685 (ttt) REVERT: K 5 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7370 (ptm160) REVERT: K 50 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8005 (mt) REVERT: L 25 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8814 (tt) REVERT: L 81 MET cc_start: 0.7476 (ppp) cc_final: 0.6750 (ppp) REVERT: M 26 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8407 (ttpt) REVERT: M 39 ILE cc_start: 0.8873 (mp) cc_final: 0.8659 (mm) REVERT: M 81 MET cc_start: 0.8048 (ppp) cc_final: 0.7793 (ppp) REVERT: O 8 ILE cc_start: 0.9127 (mm) cc_final: 0.8765 (tp) REVERT: O 20 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (tm) REVERT: O 26 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8186 (ttpt) REVERT: O 67 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7099 (pm20) outliers start: 148 outliers final: 101 residues processed: 481 average time/residue: 0.2859 time to fit residues: 185.8628 Evaluate side-chains 484 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 376 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 LYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 40.0000 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 74 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 91 GLN N 86 GLN N 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085803 restraints weight = 38308.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087370 restraints weight = 12841.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088267 restraints weight = 5669.439| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10695 Z= 0.166 Angle : 0.796 8.389 14385 Z= 0.375 Chirality : 0.042 0.273 1680 Planarity : 0.005 0.075 1860 Dihedral : 7.004 58.555 1516 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 12.79 % Allowed : 32.42 % Favored : 54.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1335 helix: -1.08 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.37 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 90 PHE 0.011 0.002 PHE I 59 TYR 0.011 0.002 TYR J 64 ARG 0.004 0.000 ARG L 5 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 475) hydrogen bonds : angle 5.79117 ( 1404) covalent geometry : bond 0.00360 (10695) covalent geometry : angle 0.79561 (14385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 399 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6920 (mtm) cc_final: 0.6317 (ttt) REVERT: A 8 ILE cc_start: 0.8762 (mm) cc_final: 0.8043 (tp) REVERT: C 1 MET cc_start: 0.6137 (mtm) cc_final: 0.5238 (ttp) REVERT: D 1 MET cc_start: 0.7264 (mtm) cc_final: 0.6046 (ttt) REVERT: D 10 ASP cc_start: 0.8955 (m-30) cc_final: 0.8479 (t0) REVERT: E 8 ILE cc_start: 0.8458 (mm) cc_final: 0.8193 (tp) REVERT: F 1 MET cc_start: 0.6780 (mtm) cc_final: 0.6201 (ttt) REVERT: F 8 ILE cc_start: 0.8908 (mm) cc_final: 0.8518 (tp) REVERT: F 20 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8404 (tm) REVERT: G 8 ILE cc_start: 0.8778 (mm) cc_final: 0.8490 (tp) REVERT: G 26 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8262 (ttpt) REVERT: G 59 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8214 (t80) REVERT: H 81 MET cc_start: 0.7723 (ppp) cc_final: 0.7228 (ppp) REVERT: I 1 MET cc_start: 0.6926 (mtt) cc_final: 0.5788 (ttt) REVERT: I 67 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6787 (mm-30) REVERT: J 1 MET cc_start: 0.7314 (mtm) cc_final: 0.5216 (ttt) REVERT: J 75 ASP cc_start: 0.7438 (t0) cc_final: 0.7064 (p0) REVERT: K 1 MET cc_start: 0.7206 (mtt) cc_final: 0.6672 (ttt) REVERT: K 5 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7344 (ptm160) REVERT: L 25 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8903 (tt) REVERT: L 81 MET cc_start: 0.7430 (ppp) cc_final: 0.6776 (ppp) REVERT: M 1 MET cc_start: 0.4412 (ttt) cc_final: 0.3409 (ttm) REVERT: M 26 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8521 (ttpt) REVERT: M 39 ILE cc_start: 0.8867 (mp) cc_final: 0.8588 (mm) REVERT: M 48 ASP cc_start: 0.7720 (t0) cc_final: 0.7420 (t0) REVERT: M 81 MET cc_start: 0.7972 (ppp) cc_final: 0.7646 (ppp) REVERT: O 8 ILE cc_start: 0.9163 (mm) cc_final: 0.8858 (tp) REVERT: O 20 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8094 (tm) REVERT: O 26 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8116 (ttpt) REVERT: O 51 ASP cc_start: 0.8275 (m-30) cc_final: 0.8047 (m-30) outliers start: 140 outliers final: 103 residues processed: 481 average time/residue: 0.2928 time to fit residues: 192.9073 Evaluate side-chains 485 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 376 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 26 LYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 76 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085377 restraints weight = 39542.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086828 restraints weight = 12299.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087685 restraints weight = 5231.189| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.7417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10695 Z= 0.155 Angle : 0.820 13.127 14385 Z= 0.379 Chirality : 0.042 0.235 1680 Planarity : 0.005 0.044 1860 Dihedral : 6.960 59.995 1516 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 12.15 % Allowed : 34.43 % Favored : 53.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1335 helix: -1.06 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.39 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.012 0.002 PHE D 23 TYR 0.013 0.002 TYR N 64 ARG 0.003 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 475) hydrogen bonds : angle 5.73658 ( 1404) covalent geometry : bond 0.00339 (10695) covalent geometry : angle 0.81990 (14385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 404 time to evaluate : 1.275 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: A 1 MET cc_start: 0.6858 (mtm) cc_final: 0.5206 (ttt) REVERT: A 26 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8493 (ttpt) REVERT: C 1 MET cc_start: 0.6144 (mtm) cc_final: 0.5229 (ttp) REVERT: D 1 MET cc_start: 0.7237 (mtm) cc_final: 0.6094 (ttt) REVERT: D 10 ASP cc_start: 0.8900 (m-30) cc_final: 0.8479 (t0) REVERT: E 8 ILE cc_start: 0.8650 (mm) cc_final: 0.8383 (tp) REVERT: E 76 MET cc_start: 0.5009 (ttt) cc_final: 0.4137 (ttt) REVERT: F 1 MET cc_start: 0.6806 (mtm) cc_final: 0.6192 (ttt) REVERT: F 8 ILE cc_start: 0.8879 (mm) cc_final: 0.8446 (tp) REVERT: F 20 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8383 (tm) REVERT: F 81 MET cc_start: 0.7130 (ppp) cc_final: 0.6717 (ppp) REVERT: G 8 ILE cc_start: 0.8777 (mm) cc_final: 0.8442 (tp) REVERT: G 26 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8215 (ttpt) REVERT: G 59 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8142 (t80) REVERT: H 81 MET cc_start: 0.7761 (ppp) cc_final: 0.7227 (ppp) REVERT: I 1 MET cc_start: 0.7013 (mtt) cc_final: 0.5910 (ttt) REVERT: I 59 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8047 (t80) REVERT: I 67 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6866 (mm-30) REVERT: J 1 MET cc_start: 0.7309 (mtm) cc_final: 0.5407 (ttt) REVERT: J 75 ASP cc_start: 0.7350 (t0) cc_final: 0.7082 (p0) REVERT: K 1 MET cc_start: 0.7275 (mtt) cc_final: 0.6601 (ttt) REVERT: K 3 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6032 (tmt170) REVERT: K 75 ASP cc_start: 0.7002 (m-30) cc_final: 0.6797 (m-30) REVERT: L 81 MET cc_start: 0.7398 (ppp) cc_final: 0.6800 (ppp) REVERT: M 1 MET cc_start: 0.4264 (ttt) cc_final: 0.3400 (ttm) REVERT: M 3 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7549 (tpt-90) REVERT: M 26 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8325 (ttpt) REVERT: M 39 ILE cc_start: 0.8848 (mp) cc_final: 0.8563 (mm) REVERT: M 48 ASP cc_start: 0.7738 (t0) cc_final: 0.7463 (t0) REVERT: M 81 MET cc_start: 0.7842 (ppp) cc_final: 0.7443 (ppp) REVERT: N 81 MET cc_start: 0.7947 (ppp) cc_final: 0.7211 (ppp) REVERT: O 8 ILE cc_start: 0.9209 (mm) cc_final: 0.8937 (tp) REVERT: O 26 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (ttpt) outliers start: 133 outliers final: 99 residues processed: 478 average time/residue: 0.2827 time to fit residues: 183.6587 Evaluate side-chains 487 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 382 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 26 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 76 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 20 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086537 restraints weight = 38796.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088010 restraints weight = 12846.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088881 restraints weight = 5748.822| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.7698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10695 Z= 0.147 Angle : 0.820 11.859 14385 Z= 0.381 Chirality : 0.042 0.230 1680 Planarity : 0.005 0.051 1860 Dihedral : 6.878 59.991 1516 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 11.87 % Allowed : 34.89 % Favored : 53.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1335 helix: -1.10 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.45 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 90 PHE 0.009 0.002 PHE I 59 TYR 0.013 0.002 TYR N 64 ARG 0.008 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 475) hydrogen bonds : angle 5.72811 ( 1404) covalent geometry : bond 0.00325 (10695) covalent geometry : angle 0.81968 (14385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 412 time to evaluate : 1.148 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: A 1 MET cc_start: 0.6961 (mtm) cc_final: 0.5453 (ttt) REVERT: A 26 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8507 (ttpt) REVERT: C 1 MET cc_start: 0.6045 (mtm) cc_final: 0.5104 (ttp) REVERT: D 1 MET cc_start: 0.7128 (mtm) cc_final: 0.6463 (ttt) REVERT: D 10 ASP cc_start: 0.8737 (m-30) cc_final: 0.8346 (t0) REVERT: E 8 ILE cc_start: 0.8642 (mm) cc_final: 0.8374 (tp) REVERT: F 1 MET cc_start: 0.6661 (mtm) cc_final: 0.6085 (ttt) REVERT: F 8 ILE cc_start: 0.8876 (mm) cc_final: 0.8414 (tp) REVERT: F 20 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8406 (tm) REVERT: F 81 MET cc_start: 0.7204 (ppp) cc_final: 0.6998 (ppp) REVERT: G 8 ILE cc_start: 0.8922 (mm) cc_final: 0.8583 (tp) REVERT: G 26 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8199 (ttpt) REVERT: G 59 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8162 (t80) REVERT: G 76 MET cc_start: 0.5629 (ttt) cc_final: 0.5303 (ttt) REVERT: H 81 MET cc_start: 0.7629 (ppp) cc_final: 0.7139 (ppp) REVERT: I 1 MET cc_start: 0.7094 (mtt) cc_final: 0.5902 (ttt) REVERT: I 52 LEU cc_start: 0.8939 (tp) cc_final: 0.8723 (tp) REVERT: I 59 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7722 (t80) REVERT: I 67 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6971 (mm-30) REVERT: J 1 MET cc_start: 0.7318 (mtm) cc_final: 0.5503 (ttt) REVERT: J 81 MET cc_start: 0.7082 (ppp) cc_final: 0.6588 (ppp) REVERT: K 1 MET cc_start: 0.7356 (mtt) cc_final: 0.6599 (ttt) REVERT: K 3 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6030 (tmt170) REVERT: K 5 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7282 (ptm160) REVERT: L 81 MET cc_start: 0.7306 (ppp) cc_final: 0.6770 (ppp) REVERT: M 1 MET cc_start: 0.4293 (ttt) cc_final: 0.3433 (ttm) REVERT: M 20 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8593 (tm) REVERT: M 26 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8431 (ttpt) REVERT: M 39 ILE cc_start: 0.8850 (mp) cc_final: 0.8557 (mm) REVERT: M 81 MET cc_start: 0.7674 (ppp) cc_final: 0.6957 (ppp) REVERT: N 47 MET cc_start: 0.6894 (mmt) cc_final: 0.6640 (tpt) REVERT: N 81 MET cc_start: 0.7914 (ppp) cc_final: 0.7221 (ppp) REVERT: O 8 ILE cc_start: 0.9230 (mm) cc_final: 0.8973 (tp) REVERT: O 24 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8826 (ptmt) outliers start: 130 outliers final: 97 residues processed: 486 average time/residue: 0.2280 time to fit residues: 150.9792 Evaluate side-chains 487 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 384 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 120 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 chunk 130 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087085 restraints weight = 39771.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088635 restraints weight = 13149.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089552 restraints weight = 5941.463| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10695 Z= 0.139 Angle : 0.842 11.900 14385 Z= 0.389 Chirality : 0.042 0.307 1680 Planarity : 0.004 0.046 1860 Dihedral : 6.791 59.477 1516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 9.95 % Allowed : 37.53 % Favored : 52.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1335 helix: -1.08 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.48 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.010 0.002 PHE G 59 TYR 0.010 0.001 TYR O 64 ARG 0.008 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 475) hydrogen bonds : angle 5.70503 ( 1404) covalent geometry : bond 0.00313 (10695) covalent geometry : angle 0.84241 (14385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 397 time to evaluate : 1.230 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: A 1 MET cc_start: 0.6971 (mtm) cc_final: 0.6111 (ttt) REVERT: B 1 MET cc_start: 0.3673 (ttt) cc_final: 0.3057 (ttm) REVERT: C 1 MET cc_start: 0.6149 (mtm) cc_final: 0.4059 (ttt) REVERT: D 1 MET cc_start: 0.7117 (mtm) cc_final: 0.6500 (ttt) REVERT: D 10 ASP cc_start: 0.8661 (m-30) cc_final: 0.8261 (t0) REVERT: E 8 ILE cc_start: 0.8606 (mm) cc_final: 0.8343 (tp) REVERT: F 1 MET cc_start: 0.6689 (mtm) cc_final: 0.6136 (ttt) REVERT: F 8 ILE cc_start: 0.8822 (mm) cc_final: 0.8380 (tp) REVERT: F 20 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8354 (tm) REVERT: F 81 MET cc_start: 0.7180 (ppp) cc_final: 0.6888 (ppp) REVERT: G 26 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8170 (ttpt) REVERT: G 59 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8061 (t80) REVERT: G 76 MET cc_start: 0.5672 (ttt) cc_final: 0.5368 (ttt) REVERT: H 81 MET cc_start: 0.7632 (ppp) cc_final: 0.7093 (ppp) REVERT: I 1 MET cc_start: 0.7085 (mtt) cc_final: 0.5869 (ttt) REVERT: I 8 ILE cc_start: 0.8673 (mm) cc_final: 0.8062 (tp) REVERT: I 59 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7632 (t80) REVERT: I 67 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6749 (mm-30) REVERT: J 1 MET cc_start: 0.7115 (mtm) cc_final: 0.5340 (ttt) REVERT: J 10 ASP cc_start: 0.9396 (m-30) cc_final: 0.9181 (m-30) REVERT: J 81 MET cc_start: 0.7106 (ppp) cc_final: 0.6520 (ppp) REVERT: K 1 MET cc_start: 0.7197 (mtt) cc_final: 0.6540 (ttt) REVERT: K 5 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7255 (ptm160) REVERT: L 81 MET cc_start: 0.7483 (ppp) cc_final: 0.7038 (ppp) REVERT: M 1 MET cc_start: 0.4129 (ttt) cc_final: 0.3266 (ttm) REVERT: M 81 MET cc_start: 0.7480 (ppp) cc_final: 0.6956 (ppp) REVERT: N 81 MET cc_start: 0.7915 (ppp) cc_final: 0.7222 (ppp) REVERT: O 8 ILE cc_start: 0.9186 (mm) cc_final: 0.8917 (tp) REVERT: O 80 GLU cc_start: 0.7749 (tt0) cc_final: 0.7524 (tt0) outliers start: 109 outliers final: 85 residues processed: 461 average time/residue: 0.2553 time to fit residues: 158.9213 Evaluate side-chains 467 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 378 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086156 restraints weight = 38991.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087699 restraints weight = 13216.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088552 restraints weight = 5872.324| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.8133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10695 Z= 0.159 Angle : 0.893 12.694 14385 Z= 0.412 Chirality : 0.044 0.310 1680 Planarity : 0.005 0.042 1860 Dihedral : 6.781 59.289 1516 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 8.77 % Allowed : 38.36 % Favored : 52.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1335 helix: -1.05 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.42 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.014 0.002 PHE D 23 TYR 0.013 0.002 TYR L 64 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 475) hydrogen bonds : angle 5.85878 ( 1404) covalent geometry : bond 0.00357 (10695) covalent geometry : angle 0.89258 (14385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 379 time to evaluate : 1.244 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: A 1 MET cc_start: 0.6852 (mtm) cc_final: 0.6021 (ttt) REVERT: B 1 MET cc_start: 0.3836 (ttt) cc_final: 0.3307 (ttm) REVERT: C 1 MET cc_start: 0.6180 (mtm) cc_final: 0.5098 (ttp) REVERT: D 1 MET cc_start: 0.6997 (mtm) cc_final: 0.6419 (ttt) REVERT: D 3 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7779 (tpp-160) REVERT: D 10 ASP cc_start: 0.8752 (m-30) cc_final: 0.8349 (t0) REVERT: E 8 ILE cc_start: 0.8659 (mm) cc_final: 0.8380 (tp) REVERT: E 67 GLU cc_start: 0.8726 (pt0) cc_final: 0.8442 (tp30) REVERT: F 1 MET cc_start: 0.6628 (mtm) cc_final: 0.6033 (ttt) REVERT: F 8 ILE cc_start: 0.8838 (mm) cc_final: 0.8372 (tp) REVERT: F 20 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8515 (tm) REVERT: F 26 LYS cc_start: 0.7988 (tptt) cc_final: 0.7684 (ttpt) REVERT: F 81 MET cc_start: 0.7326 (ppp) cc_final: 0.7081 (ppp) REVERT: G 8 ILE cc_start: 0.8972 (mm) cc_final: 0.8454 (tp) REVERT: G 26 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8230 (ttpt) REVERT: G 59 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8172 (t80) REVERT: H 81 MET cc_start: 0.7567 (ppp) cc_final: 0.7116 (ppp) REVERT: I 1 MET cc_start: 0.7081 (mtt) cc_final: 0.5846 (ttt) REVERT: I 59 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7565 (t80) REVERT: I 67 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6778 (mm-30) REVERT: J 1 MET cc_start: 0.7014 (mtm) cc_final: 0.5284 (ttt) REVERT: J 10 ASP cc_start: 0.9400 (m-30) cc_final: 0.9170 (m-30) REVERT: J 81 MET cc_start: 0.7102 (ppp) cc_final: 0.6459 (ppp) REVERT: K 1 MET cc_start: 0.7200 (mtt) cc_final: 0.6522 (ttt) REVERT: K 3 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7114 (tpp-160) REVERT: K 5 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7292 (ptm160) REVERT: L 81 MET cc_start: 0.7429 (ppp) cc_final: 0.6985 (ppp) REVERT: M 1 MET cc_start: 0.4268 (ttt) cc_final: 0.3425 (ttm) REVERT: M 81 MET cc_start: 0.7595 (ppp) cc_final: 0.6896 (ppp) REVERT: N 75 ASP cc_start: 0.7611 (t0) cc_final: 0.7301 (m-30) REVERT: N 81 MET cc_start: 0.7992 (ppp) cc_final: 0.7368 (ppp) REVERT: O 8 ILE cc_start: 0.9179 (mm) cc_final: 0.8894 (tp) outliers start: 96 outliers final: 78 residues processed: 435 average time/residue: 0.2489 time to fit residues: 146.7366 Evaluate side-chains 460 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 377 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 125 optimal weight: 20.0000 chunk 109 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085753 restraints weight = 39081.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087171 restraints weight = 12075.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087956 restraints weight = 5131.380| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.8286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10695 Z= 0.159 Angle : 0.897 12.802 14385 Z= 0.418 Chirality : 0.044 0.315 1680 Planarity : 0.005 0.042 1860 Dihedral : 6.812 57.696 1516 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 8.31 % Allowed : 39.36 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1335 helix: -1.09 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.32 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 90 PHE 0.011 0.002 PHE E 59 TYR 0.015 0.002 TYR O 64 ARG 0.008 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 475) hydrogen bonds : angle 5.90912 ( 1404) covalent geometry : bond 0.00359 (10695) covalent geometry : angle 0.89722 (14385) =============================================================================== Job complete usr+sys time: 3980.44 seconds wall clock time: 70 minutes 56.64 seconds (4256.64 seconds total)