Starting phenix.real_space_refine on Wed Sep 17 17:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j63_5830/09_2025/3j63_5830.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j63_5830/09_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_5830/09_2025/3j63_5830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j63_5830/09_2025/3j63_5830.map" model { file = "/net/cci-nas-00/data/ceres_data/3j63_5830/09_2025/3j63_5830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j63_5830/09_2025/3j63_5830.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.62, per 1000 atoms: 0.25 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: 1.13 Conformation dependent library (CDL) restraints added in 399.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.33 Time building geometry restraints manager: 1.45 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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: 0.060 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- 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 : 54.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 5 TYR 0.028 0.004 TYR O 36 PHE 0.008 0.002 PHE B 23 HIS 0.001 0.000 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00457 (10695) covalent geometry : angle 1.25221 (14385) hydrogen bonds : bond 0.33265 ( 475) hydrogen bonds : angle 10.76444 ( 1404) *********************** 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 : 0.372 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: 0.1019 time to fit residues: 77.8877 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 : 0.353 ------------------------------------------------------------------------------- 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 98 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 B 79 GLN E 14 ASN F 14 ASN G 71 ASN L 14 ASN N 14 ASN O 14 ASN O 90 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108205 restraints weight = 34422.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110335 restraints weight = 15916.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111617 restraints weight = 8735.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112507 restraints weight = 5396.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113130 restraints weight = 3598.951| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 0.99 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10695 Z= 0.212 Angle : 0.913 10.497 14385 Z= 0.446 Chirality : 0.043 0.201 1680 Planarity : 0.007 0.076 1860 Dihedral : 9.365 59.004 1595 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 8.40 % Allowed : 26.85 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.21), residues: 1335 helix: -2.36 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.48 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 33 TYR 0.022 0.002 TYR G 64 PHE 0.028 0.003 PHE B 59 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00426 (10695) covalent geometry : angle 0.91345 (14385) hydrogen bonds : bond 0.06858 ( 475) hydrogen bonds : angle 7.17350 ( 1404) *********************** 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 519 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 427 time to evaluate : 0.414 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: A 1 MET cc_start: 0.6802 (mtm) cc_final: 0.6483 (ttt) REVERT: B 1 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6137 (ttt) REVERT: B 76 MET cc_start: 0.5367 (ttt) cc_final: 0.5144 (tmm) REVERT: C 1 MET cc_start: 0.6495 (mtm) cc_final: 0.5864 (ttp) REVERT: C 39 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (mt) REVERT: D 1 MET cc_start: 0.7194 (mtm) cc_final: 0.5934 (ttt) REVERT: E 8 ILE cc_start: 0.8671 (mm) cc_final: 0.8276 (tp) REVERT: F 1 MET cc_start: 0.7252 (mtm) cc_final: 0.6166 (ttt) REVERT: F 51 ASP cc_start: 0.8201 (m-30) cc_final: 0.7915 (m-30) REVERT: F 58 SER cc_start: 0.8710 (m) cc_final: 0.8347 (p) REVERT: H 8 ILE cc_start: 0.9234 (mm) cc_final: 0.8939 (tp) REVERT: H 38 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6530 (mtt180) REVERT: H 73 LEU cc_start: 0.8687 (mt) cc_final: 0.8171 (tp) REVERT: I 1 MET cc_start: 0.7371 (mtt) cc_final: 0.5456 (ttt) REVERT: I 67 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6760 (mm-30) REVERT: J 1 MET cc_start: 0.7445 (mtm) cc_final: 0.5419 (ttt) REVERT: J 51 ASP cc_start: 0.7293 (m-30) cc_final: 0.6719 (m-30) REVERT: J 79 GLN cc_start: 0.6200 (mp10) cc_final: 0.5935 (mp10) REVERT: K 1 MET cc_start: 0.7390 (mtt) cc_final: 0.6234 (ttm) REVERT: K 5 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7579 (ptm160) REVERT: K 50 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7708 (mt) REVERT: K 51 ASP cc_start: 0.8057 (m-30) cc_final: 0.7618 (m-30) REVERT: L 50 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8106 (mt) REVERT: L 76 MET cc_start: 0.5174 (ttt) cc_final: 0.4868 (ttt) REVERT: M 51 ASP cc_start: 0.8668 (m-30) cc_final: 0.8287 (m-30) REVERT: O 1 MET cc_start: 0.7918 (mtt) cc_final: 0.6494 (ttt) REVERT: O 8 ILE cc_start: 0.9197 (mm) cc_final: 0.8694 (tp) REVERT: O 24 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8628 (mtpp) REVERT: O 26 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8105 (ttpt) REVERT: O 51 ASP cc_start: 0.8010 (m-30) cc_final: 0.7203 (m-30) outliers start: 92 outliers final: 59 residues processed: 477 average time/residue: 0.1030 time to fit residues: 67.2516 Evaluate side-chains 427 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 B residue 1 MET Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 16 THR 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 C residue 69 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 16 THR 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 F residue 69 THR 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 16 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain I residue 16 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 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 53 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 50 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 16 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 53 THR 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 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 72 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095003 restraints weight = 38727.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096897 restraints weight = 14943.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098046 restraints weight = 7292.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098771 restraints weight = 4078.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099233 restraints weight = 2508.744| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10695 Z= 0.137 Angle : 0.780 7.083 14385 Z= 0.372 Chirality : 0.040 0.244 1680 Planarity : 0.005 0.061 1860 Dihedral : 7.757 59.367 1527 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 10.32 % Allowed : 29.77 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.22), residues: 1335 helix: -1.35 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.16 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 5 TYR 0.017 0.002 TYR O 64 PHE 0.013 0.002 PHE B 59 HIS 0.002 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00290 (10695) covalent geometry : angle 0.77972 (14385) hydrogen bonds : bond 0.04894 ( 475) hydrogen bonds : angle 6.09050 ( 1404) *********************** 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 521 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 408 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7070 (mtm) cc_final: 0.6566 (ttt) REVERT: B 1 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.6077 (ttt) REVERT: C 1 MET cc_start: 0.6428 (mtm) cc_final: 0.5808 (mtp) REVERT: C 26 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8318 (ttpt) REVERT: D 1 MET cc_start: 0.7304 (mtm) cc_final: 0.5880 (ttt) REVERT: D 10 ASP cc_start: 0.8626 (m-30) cc_final: 0.8245 (t0) REVERT: E 8 ILE cc_start: 0.8681 (mm) cc_final: 0.8397 (tp) REVERT: F 1 MET cc_start: 0.6850 (mtm) cc_final: 0.5965 (ttt) REVERT: F 8 ILE cc_start: 0.8889 (mm) cc_final: 0.8484 (tp) REVERT: F 20 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8294 (tm) REVERT: F 51 ASP cc_start: 0.7769 (m-30) cc_final: 0.7342 (m-30) REVERT: F 58 SER cc_start: 0.8539 (m) cc_final: 0.8327 (p) REVERT: G 5 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8333 (ptp-170) REVERT: G 52 LEU cc_start: 0.8246 (tp) cc_final: 0.7984 (tp) REVERT: I 1 MET cc_start: 0.7241 (mtt) cc_final: 0.5655 (ttt) REVERT: I 39 ILE cc_start: 0.8977 (mp) cc_final: 0.8714 (mm) REVERT: I 67 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6872 (mm-30) REVERT: J 1 MET cc_start: 0.7548 (mtm) cc_final: 0.5234 (ttt) REVERT: J 51 ASP cc_start: 0.7655 (m-30) cc_final: 0.7337 (m-30) REVERT: K 1 MET cc_start: 0.7409 (mtt) cc_final: 0.6192 (ttm) REVERT: K 5 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7355 (ptm160) REVERT: K 51 ASP cc_start: 0.8188 (m-30) cc_final: 0.7929 (m-30) REVERT: M 26 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8439 (ttpt) REVERT: M 39 ILE cc_start: 0.8770 (mp) cc_final: 0.8429 (mm) REVERT: M 80 GLU cc_start: 0.7440 (tt0) cc_final: 0.7185 (tt0) REVERT: O 1 MET cc_start: 0.7672 (mtt) cc_final: 0.6289 (ttt) REVERT: O 8 ILE cc_start: 0.9248 (mm) cc_final: 0.8862 (tp) REVERT: O 51 ASP cc_start: 0.8183 (m-30) cc_final: 0.7707 (m-30) outliers start: 113 outliers final: 68 residues processed: 470 average time/residue: 0.1115 time to fit residues: 71.1960 Evaluate side-chains 441 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 63 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU 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 53 THR Chi-restraints excluded: chain D residue 56 LEU 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 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 59 PHE Chi-restraints excluded: chain G residue 5 ARG 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 59 PHE 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 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 26 LYS 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 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 73 LEU 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 N residue 5 ARG 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 N residue 59 PHE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.093671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.088899 restraints weight = 39226.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090603 restraints weight = 14133.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091637 restraints weight = 6667.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092286 restraints weight = 3645.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092695 restraints weight = 2200.636| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6521 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= 0.138 Angle : 0.760 14.113 14385 Z= 0.360 Chirality : 0.039 0.191 1680 Planarity : 0.005 0.054 1860 Dihedral : 7.368 59.958 1525 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 11.05 % Allowed : 30.14 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.23), residues: 1335 helix: -1.21 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 0.98 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 74 TYR 0.012 0.002 TYR C 64 PHE 0.007 0.002 PHE C 59 HIS 0.002 0.001 HIS I 90 Details of bonding type rmsd covalent geometry : bond 0.00302 (10695) covalent geometry : angle 0.75965 (14385) hydrogen bonds : bond 0.04556 ( 475) hydrogen bonds : angle 5.78221 ( 1404) *********************** 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 531 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 410 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6937 (mtm) cc_final: 0.6426 (ttt) REVERT: A 26 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8341 (ttpt) REVERT: B 1 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5952 (ttt) REVERT: B 20 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8741 (tm) REVERT: B 81 MET cc_start: 0.7341 (ppp) cc_final: 0.7080 (ppp) REVERT: C 1 MET cc_start: 0.6341 (mtm) cc_final: 0.5620 (mtp) REVERT: C 39 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8576 (mt) REVERT: D 1 MET cc_start: 0.7581 (mtm) cc_final: 0.5900 (ttt) REVERT: D 10 ASP cc_start: 0.8722 (m-30) cc_final: 0.8348 (t0) REVERT: E 8 ILE cc_start: 0.8607 (mm) cc_final: 0.8369 (tp) REVERT: E 76 MET cc_start: 0.5339 (ttp) cc_final: 0.5027 (ttp) REVERT: F 1 MET cc_start: 0.7023 (mtm) cc_final: 0.5990 (ttt) REVERT: F 8 ILE cc_start: 0.8857 (mm) cc_final: 0.8471 (tp) REVERT: F 20 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8387 (tm) REVERT: F 34 GLU cc_start: 0.6503 (pm20) cc_final: 0.4995 (tm-30) REVERT: F 51 ASP cc_start: 0.7730 (m-30) cc_final: 0.7394 (m-30) REVERT: F 58 SER cc_start: 0.8632 (m) cc_final: 0.8429 (p) REVERT: G 8 ILE cc_start: 0.9016 (mm) cc_final: 0.8684 (tp) REVERT: G 26 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8339 (ttpt) REVERT: G 59 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8202 (t80) REVERT: G 81 MET cc_start: 0.7616 (ppp) cc_final: 0.7056 (ppp) REVERT: I 1 MET cc_start: 0.7216 (mtt) cc_final: 0.5789 (ttt) REVERT: I 67 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6716 (mm-30) REVERT: J 1 MET cc_start: 0.7368 (mtm) cc_final: 0.5468 (ttt) REVERT: K 1 MET cc_start: 0.7304 (mtt) cc_final: 0.5944 (ttm) REVERT: K 5 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7336 (ptm160) REVERT: L 39 ILE cc_start: 0.9170 (mp) cc_final: 0.8949 (mm) REVERT: L 81 MET cc_start: 0.7421 (ppp) cc_final: 0.6491 (ppp) REVERT: O 1 MET cc_start: 0.7436 (mtt) cc_final: 0.6115 (ttt) REVERT: O 8 ILE cc_start: 0.9189 (mm) cc_final: 0.8783 (tp) REVERT: O 39 ILE cc_start: 0.8460 (mp) cc_final: 0.8192 (mm) REVERT: O 51 ASP cc_start: 0.8125 (m-30) cc_final: 0.7814 (m-30) outliers start: 121 outliers final: 86 residues processed: 484 average time/residue: 0.1129 time to fit residues: 73.8979 Evaluate side-chains 469 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 377 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 B residue 1 MET 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 C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 44 LEU 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 D residue 73 LEU 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 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 51 ASP 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 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 48 ASP 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 J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 26 LYS 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 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 L residue 16 THR 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 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 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 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 113 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 0.0470 chunk 49 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 30.0000 overall best weight: 6.4086 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086804 restraints weight = 39205.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088369 restraints weight = 13006.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089268 restraints weight = 5705.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089798 restraints weight = 2903.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090119 restraints weight = 1641.070| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10695 Z= 0.162 Angle : 0.764 11.282 14385 Z= 0.360 Chirality : 0.039 0.173 1680 Planarity : 0.005 0.048 1860 Dihedral : 7.350 57.278 1523 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 12.97 % Allowed : 29.77 % Favored : 57.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1335 helix: -1.21 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.34 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.011 0.002 TYR F 64 PHE 0.011 0.002 PHE O 59 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00353 (10695) covalent geometry : angle 0.76408 (14385) hydrogen bonds : bond 0.04747 ( 475) hydrogen bonds : angle 5.78175 ( 1404) *********************** 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 539 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 397 time to evaluate : 0.500 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: 0.6917 (mtm) cc_final: 0.6218 (ttt) REVERT: B 20 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8680 (tm) REVERT: B 81 MET cc_start: 0.7418 (ppp) cc_final: 0.7063 (ppp) REVERT: C 1 MET cc_start: 0.6291 (mtm) cc_final: 0.5878 (mtp) REVERT: C 24 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8595 (pttt) REVERT: D 1 MET cc_start: 0.7148 (mtm) cc_final: 0.5771 (ttt) REVERT: D 10 ASP cc_start: 0.8851 (m-30) cc_final: 0.8502 (t0) REVERT: E 8 ILE cc_start: 0.8549 (mm) cc_final: 0.8299 (tp) REVERT: F 1 MET cc_start: 0.7139 (mtm) cc_final: 0.6195 (ttt) REVERT: F 8 ILE cc_start: 0.8870 (mm) cc_final: 0.8442 (tp) REVERT: F 67 GLU cc_start: 0.8403 (pt0) cc_final: 0.8113 (tp30) REVERT: F 81 MET cc_start: 0.8002 (tmm) cc_final: 0.7322 (ppp) REVERT: G 26 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8459 (ttpt) REVERT: G 39 ILE cc_start: 0.8765 (mp) cc_final: 0.8514 (mm) REVERT: G 59 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8186 (t80) REVERT: H 81 MET cc_start: 0.7553 (ppp) cc_final: 0.6996 (ppp) REVERT: I 1 MET cc_start: 0.7259 (mtt) cc_final: 0.6005 (ttt) REVERT: I 39 ILE cc_start: 0.8959 (mp) cc_final: 0.8752 (mm) REVERT: I 67 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6622 (mm-30) REVERT: J 1 MET cc_start: 0.7173 (mtm) cc_final: 0.5278 (ttt) REVERT: K 1 MET cc_start: 0.7287 (mtt) cc_final: 0.6228 (ttt) REVERT: K 5 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7360 (ptm160) REVERT: K 50 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7893 (mt) REVERT: L 25 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8936 (tt) REVERT: L 81 MET cc_start: 0.7270 (ppp) cc_final: 0.6546 (ppp) REVERT: M 26 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8449 (ttpt) REVERT: M 81 MET cc_start: 0.7944 (ppp) cc_final: 0.7612 (ppp) REVERT: N 48 ASP cc_start: 0.7377 (t0) cc_final: 0.7169 (t70) REVERT: N 72 VAL cc_start: 0.8463 (p) cc_final: 0.8113 (p) REVERT: O 8 ILE cc_start: 0.9206 (mm) cc_final: 0.8843 (tp) REVERT: O 51 ASP cc_start: 0.8126 (m-30) cc_final: 0.7926 (m-30) outliers start: 142 outliers final: 95 residues processed: 478 average time/residue: 0.1102 time to fit residues: 72.6484 Evaluate side-chains 480 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 380 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE 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 44 LEU 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 16 THR Chi-restraints excluded: chain D residue 30 VAL 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 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 28 LEU Chi-restraints excluded: chain F residue 39 ILE 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 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 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 H residue 72 VAL 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 48 ASP 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 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 72 VAL 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 63 THR Chi-restraints excluded: chain K residue 67 GLU 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 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 53 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE 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 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE 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 93 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN N 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086020 restraints weight = 39633.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087470 restraints weight = 12325.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088280 restraints weight = 5132.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088742 restraints weight = 2551.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089042 restraints weight = 1432.706| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10695 Z= 0.167 Angle : 0.791 10.229 14385 Z= 0.371 Chirality : 0.040 0.219 1680 Planarity : 0.005 0.073 1860 Dihedral : 7.172 53.332 1520 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 12.15 % Allowed : 32.33 % Favored : 55.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1335 helix: -1.06 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.51 (0.35), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 5 TYR 0.018 0.002 TYR B 64 PHE 0.011 0.002 PHE M 59 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00364 (10695) covalent geometry : angle 0.79113 (14385) hydrogen bonds : bond 0.04792 ( 475) hydrogen bonds : angle 5.80338 ( 1404) *********************** 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 533 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 400 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6962 (mtm) cc_final: 0.6381 (ttt) REVERT: A 8 ILE cc_start: 0.8773 (mm) cc_final: 0.7966 (tp) REVERT: B 20 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8817 (tm) REVERT: B 81 MET cc_start: 0.7537 (ppp) cc_final: 0.7091 (ppp) REVERT: C 1 MET cc_start: 0.6220 (mtm) cc_final: 0.5800 (mtp) REVERT: D 1 MET cc_start: 0.7113 (mtm) cc_final: 0.5896 (ttt) REVERT: D 3 ARG cc_start: 0.7892 (mmt180) cc_final: 0.7459 (tpt170) REVERT: D 10 ASP cc_start: 0.8838 (m-30) cc_final: 0.8483 (t0) REVERT: D 69 THR cc_start: 0.8955 (m) cc_final: 0.8743 (m) REVERT: E 8 ILE cc_start: 0.8555 (mm) cc_final: 0.8303 (tp) REVERT: F 1 MET cc_start: 0.6771 (mtm) cc_final: 0.6219 (ttt) REVERT: F 8 ILE cc_start: 0.8895 (mm) cc_final: 0.8480 (tp) REVERT: F 67 GLU cc_start: 0.8292 (pt0) cc_final: 0.7983 (tp30) REVERT: G 26 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8471 (ttpt) REVERT: G 39 ILE cc_start: 0.8850 (mp) cc_final: 0.8539 (mm) REVERT: G 59 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8132 (t80) REVERT: H 81 MET cc_start: 0.7589 (ppp) cc_final: 0.6997 (ppp) REVERT: I 1 MET cc_start: 0.6927 (mtt) cc_final: 0.5763 (ttt) REVERT: I 67 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6759 (mm-30) REVERT: J 1 MET cc_start: 0.7104 (mtm) cc_final: 0.5180 (ttt) REVERT: K 1 MET cc_start: 0.7147 (mtt) cc_final: 0.6662 (ttt) REVERT: K 5 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7344 (ptm160) REVERT: K 50 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7894 (mt) REVERT: L 81 MET cc_start: 0.7338 (ppp) cc_final: 0.6714 (ppp) REVERT: M 1 MET cc_start: 0.4268 (ttt) cc_final: 0.3026 (ttm) REVERT: M 26 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8372 (ttpt) REVERT: M 81 MET cc_start: 0.7903 (ppp) cc_final: 0.7533 (ppp) REVERT: N 48 ASP cc_start: 0.7399 (t0) cc_final: 0.7183 (t70) REVERT: O 8 ILE cc_start: 0.9222 (mm) cc_final: 0.8897 (tp) outliers start: 133 outliers final: 98 residues processed: 476 average time/residue: 0.1057 time to fit residues: 68.5516 Evaluate side-chains 488 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 386 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 44 LEU 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 28 LEU Chi-restraints excluded: chain F residue 39 ILE 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 G residue 9 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 59 PHE 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 H residue 72 VAL Chi-restraints excluded: chain H residue 73 LEU 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 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 9 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 72 VAL 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 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 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 52 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 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE 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 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 Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 129 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 91 GLN N 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086619 restraints weight = 39648.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088043 restraints weight = 11928.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088829 restraints weight = 4878.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089272 restraints weight = 2377.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089555 restraints weight = 1347.137| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 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 = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10695 Z= 0.139 Angle : 0.792 11.141 14385 Z= 0.366 Chirality : 0.041 0.305 1680 Planarity : 0.004 0.042 1860 Dihedral : 7.078 54.693 1520 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 10.32 % Allowed : 35.98 % Favored : 53.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.24), residues: 1335 helix: -0.93 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.61 (0.36), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.013 0.002 TYR J 64 PHE 0.013 0.002 PHE L 59 HIS 0.002 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00309 (10695) covalent geometry : angle 0.79246 (14385) hydrogen bonds : bond 0.04398 ( 475) hydrogen bonds : angle 5.57069 ( 1404) *********************** 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 514 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 401 time to evaluate : 0.363 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: 0.6916 (mtm) cc_final: 0.5215 (ttt) REVERT: A 8 ILE cc_start: 0.8743 (mm) cc_final: 0.8008 (tp) REVERT: B 81 MET cc_start: 0.7592 (ppp) cc_final: 0.7200 (ppp) REVERT: C 1 MET cc_start: 0.6189 (mtm) cc_final: 0.5250 (ttp) REVERT: D 1 MET cc_start: 0.7244 (mtm) cc_final: 0.6245 (ttt) REVERT: D 10 ASP cc_start: 0.8787 (m-30) cc_final: 0.8442 (t0) REVERT: E 8 ILE cc_start: 0.8566 (mm) cc_final: 0.8344 (tp) REVERT: F 1 MET cc_start: 0.6864 (mtm) cc_final: 0.6260 (ttt) REVERT: F 8 ILE cc_start: 0.8844 (mm) cc_final: 0.8432 (tp) REVERT: F 34 GLU cc_start: 0.6742 (pm20) cc_final: 0.5282 (tm-30) REVERT: F 67 GLU cc_start: 0.8311 (pt0) cc_final: 0.7967 (tp30) REVERT: F 81 MET cc_start: 0.7756 (ppp) cc_final: 0.7431 (ppp) REVERT: G 8 ILE cc_start: 0.8896 (mp) cc_final: 0.8278 (tp) REVERT: G 26 LYS cc_start: 0.8804 (ttpt) cc_final: 0.8434 (ttpt) REVERT: G 51 ASP cc_start: 0.8408 (m-30) cc_final: 0.8162 (t0) REVERT: G 59 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7959 (t80) REVERT: H 81 MET cc_start: 0.7599 (ppp) cc_final: 0.7087 (ppp) REVERT: I 1 MET cc_start: 0.7060 (mtt) cc_final: 0.5921 (ttt) REVERT: I 67 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6835 (mm-30) REVERT: J 1 MET cc_start: 0.6929 (mtm) cc_final: 0.5119 (ttt) REVERT: K 1 MET cc_start: 0.7227 (mtt) cc_final: 0.6611 (ttt) REVERT: K 50 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7904 (mt) REVERT: L 81 MET cc_start: 0.7302 (ppp) cc_final: 0.6754 (ppp) REVERT: M 1 MET cc_start: 0.3961 (ttt) cc_final: 0.2620 (ttm) REVERT: M 26 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8200 (ttpt) REVERT: M 81 MET cc_start: 0.7785 (ppp) cc_final: 0.7208 (ppp) REVERT: N 81 MET cc_start: 0.7656 (ppp) cc_final: 0.6861 (ppp) REVERT: O 8 ILE cc_start: 0.9248 (mm) cc_final: 0.8981 (tp) outliers start: 113 outliers final: 85 residues processed: 468 average time/residue: 0.1081 time to fit residues: 68.9808 Evaluate side-chains 466 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 379 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 A residue 59 PHE 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 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 44 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 VAL 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 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 16 THR Chi-restraints excluded: chain F residue 19 GLU 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 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 PHE 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 H residue 73 LEU 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 J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 28 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 50 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 9 LEU Chi-restraints excluded: chain L residue 16 THR 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 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 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 51 ASP 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 Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 37 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 114 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.091298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087790 restraints weight = 39426.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089278 restraints weight = 11936.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090059 restraints weight = 4900.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090510 restraints weight = 2350.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090803 restraints weight = 1308.195| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10695 Z= 0.134 Angle : 0.803 10.014 14385 Z= 0.370 Chirality : 0.041 0.285 1680 Planarity : 0.004 0.044 1860 Dihedral : 6.908 55.684 1520 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 9.68 % Allowed : 36.16 % Favored : 54.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.24), residues: 1335 helix: -0.92 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.61 (0.36), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 74 TYR 0.010 0.001 TYR J 64 PHE 0.010 0.002 PHE G 59 HIS 0.002 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00301 (10695) covalent geometry : angle 0.80279 (14385) hydrogen bonds : bond 0.04240 ( 475) hydrogen bonds : angle 5.48886 ( 1404) *********************** 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 508 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 402 time to evaluate : 0.398 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: 0.6768 (mtm) cc_final: 0.5266 (ttt) REVERT: A 8 ILE cc_start: 0.8794 (mm) cc_final: 0.8052 (tp) REVERT: A 26 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8268 (tttt) REVERT: A 81 MET cc_start: 0.7159 (ppp) cc_final: 0.6932 (ppp) REVERT: B 1 MET cc_start: 0.3976 (ttt) cc_final: 0.3292 (ttm) REVERT: B 39 ILE cc_start: 0.8864 (mp) cc_final: 0.8595 (mm) REVERT: B 81 MET cc_start: 0.7671 (ppp) cc_final: 0.7211 (ppp) REVERT: C 1 MET cc_start: 0.6229 (mtm) cc_final: 0.5760 (mtp) REVERT: D 1 MET cc_start: 0.7266 (mtm) cc_final: 0.6020 (ttt) REVERT: D 3 ARG cc_start: 0.7991 (mmt180) cc_final: 0.7713 (tpp-160) REVERT: D 81 MET cc_start: 0.7361 (ppp) cc_final: 0.6817 (ppp) REVERT: E 39 ILE cc_start: 0.8953 (mp) cc_final: 0.8697 (mm) REVERT: F 1 MET cc_start: 0.6869 (mtm) cc_final: 0.6280 (ttt) REVERT: F 8 ILE cc_start: 0.8845 (mm) cc_final: 0.8463 (tp) REVERT: F 34 GLU cc_start: 0.6617 (pm20) cc_final: 0.5198 (tm-30) REVERT: F 67 GLU cc_start: 0.8332 (pt0) cc_final: 0.7963 (tp30) REVERT: F 81 MET cc_start: 0.7609 (ppp) cc_final: 0.6922 (ppp) REVERT: G 8 ILE cc_start: 0.8881 (mp) cc_final: 0.8275 (tp) REVERT: G 26 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8439 (ttpt) REVERT: G 51 ASP cc_start: 0.8346 (m-30) cc_final: 0.8011 (t70) REVERT: G 59 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7821 (t80) REVERT: H 81 MET cc_start: 0.7639 (ppp) cc_final: 0.7064 (ppp) REVERT: H 84 GLN cc_start: 0.6891 (tm-30) cc_final: 0.6632 (tm-30) REVERT: I 1 MET cc_start: 0.7064 (mtt) cc_final: 0.5804 (ttt) REVERT: I 67 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6834 (mm-30) REVERT: J 1 MET cc_start: 0.6722 (mtm) cc_final: 0.4931 (ttt) REVERT: K 1 MET cc_start: 0.7380 (mtt) cc_final: 0.6636 (ttt) REVERT: K 5 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7366 (ptm160) REVERT: L 81 MET cc_start: 0.7319 (ppp) cc_final: 0.6854 (ppp) REVERT: M 1 MET cc_start: 0.4169 (ttt) cc_final: 0.2763 (ttm) REVERT: M 26 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8347 (ttpt) REVERT: M 81 MET cc_start: 0.7765 (ppp) cc_final: 0.7154 (ppp) REVERT: N 81 MET cc_start: 0.7606 (ppp) cc_final: 0.6823 (ppp) REVERT: O 8 ILE cc_start: 0.9318 (mm) cc_final: 0.9021 (tp) REVERT: O 80 GLU cc_start: 0.7831 (tt0) cc_final: 0.7630 (tt0) outliers start: 106 outliers final: 81 residues processed: 463 average time/residue: 0.1089 time to fit residues: 69.2596 Evaluate side-chains 470 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 387 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 52 LEU Chi-restraints excluded: chain B residue 59 PHE 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 44 LEU 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 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 73 LEU 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 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 45 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 G residue 9 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 PHE 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 H residue 73 LEU 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 J residue 16 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 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 51 ASP Chi-restraints excluded: chain L residue 63 THR 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 52 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 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 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 95 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 63 optimal weight: 40.0000 chunk 127 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 107 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.089101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085196 restraints weight = 39814.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086765 restraints weight = 13568.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087640 restraints weight = 6020.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088168 restraints weight = 3028.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088504 restraints weight = 1687.454| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.7900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10695 Z= 0.199 Angle : 0.883 9.758 14385 Z= 0.414 Chirality : 0.044 0.264 1680 Planarity : 0.005 0.061 1860 Dihedral : 6.976 57.583 1518 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 10.59 % Allowed : 35.89 % Favored : 53.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.24), residues: 1335 helix: -1.13 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.66 (0.36), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.014 0.002 TYR J 64 PHE 0.017 0.003 PHE E 59 HIS 0.003 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00431 (10695) covalent geometry : angle 0.88289 (14385) hydrogen bonds : bond 0.05036 ( 475) hydrogen bonds : angle 5.85518 ( 1404) *********************** 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: 116 poor density : 390 time to evaluate : 0.380 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: A 1 MET cc_start: 0.6801 (mtm) cc_final: 0.5405 (ttt) REVERT: B 1 MET cc_start: 0.4001 (ttt) cc_final: 0.3289 (ttm) REVERT: C 1 MET cc_start: 0.6140 (mtm) cc_final: 0.5697 (mtp) REVERT: D 1 MET cc_start: 0.7282 (mtm) cc_final: 0.6359 (ttt) REVERT: F 1 MET cc_start: 0.6796 (mtm) cc_final: 0.6251 (ttt) REVERT: F 8 ILE cc_start: 0.8835 (mm) cc_final: 0.8427 (tp) REVERT: F 67 GLU cc_start: 0.8165 (pt0) cc_final: 0.7869 (tp30) REVERT: F 81 MET cc_start: 0.7779 (ppp) cc_final: 0.6966 (ppp) REVERT: G 8 ILE cc_start: 0.8897 (mp) cc_final: 0.8308 (tp) REVERT: G 26 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8490 (ttpt) REVERT: G 59 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8047 (t80) REVERT: H 81 MET cc_start: 0.7603 (ppp) cc_final: 0.7025 (ppp) REVERT: I 1 MET cc_start: 0.7147 (mtt) cc_final: 0.6298 (ttt) REVERT: I 8 ILE cc_start: 0.8235 (mp) cc_final: 0.7610 (tp) REVERT: I 59 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7467 (t80) REVERT: I 67 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6846 (mm-30) REVERT: J 1 MET cc_start: 0.7131 (mtm) cc_final: 0.5364 (ttt) REVERT: J 59 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7330 (t80) REVERT: J 81 MET cc_start: 0.6898 (ppp) cc_final: 0.6339 (ppp) REVERT: K 1 MET cc_start: 0.7444 (mtt) cc_final: 0.6606 (ttt) REVERT: K 3 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.5633 (tmt170) REVERT: K 5 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7317 (ptm160) REVERT: L 81 MET cc_start: 0.7309 (ppp) cc_final: 0.6838 (ppp) REVERT: M 81 MET cc_start: 0.7677 (ppp) cc_final: 0.7002 (ppp) REVERT: N 81 MET cc_start: 0.7883 (ppp) cc_final: 0.7238 (ppp) REVERT: O 8 ILE cc_start: 0.9223 (mm) cc_final: 0.8907 (tp) REVERT: O 75 ASP cc_start: 0.8229 (t0) cc_final: 0.7706 (m-30) REVERT: O 80 GLU cc_start: 0.7751 (tt0) cc_final: 0.7520 (tt0) outliers start: 116 outliers final: 96 residues processed: 462 average time/residue: 0.1047 time to fit residues: 66.3994 Evaluate side-chains 477 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 376 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 A residue 59 PHE 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 52 LEU Chi-restraints excluded: chain B residue 59 PHE 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 44 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 30 VAL 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 73 LEU Chi-restraints excluded: chain E residue 16 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 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 PHE 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 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 73 LEU 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 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 16 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 59 PHE 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 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 9 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 51 ASP 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 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 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 34 GLU 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 85 LEU Chi-restraints excluded: chain O residue 12 LEU 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 Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 21 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.090022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.086214 restraints weight = 39971.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.087689 restraints weight = 12999.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088523 restraints weight = 5766.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089011 restraints weight = 2963.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089325 restraints weight = 1754.995| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.8197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10695 Z= 0.153 Angle : 0.886 10.506 14385 Z= 0.411 Chirality : 0.043 0.287 1680 Planarity : 0.005 0.050 1860 Dihedral : 6.795 51.042 1518 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 8.68 % Allowed : 38.17 % Favored : 53.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.24), residues: 1335 helix: -1.11 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.67 (0.36), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.011 0.002 TYR L 64 PHE 0.013 0.002 PHE D 23 HIS 0.003 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00349 (10695) covalent geometry : angle 0.88638 (14385) hydrogen bonds : bond 0.04608 ( 475) hydrogen bonds : angle 5.69583 ( 1404) ********************** 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 486 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 391 time to evaluate : 0.405 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: 0.6897 (mtm) cc_final: 0.6025 (ttt) REVERT: B 1 MET cc_start: 0.3470 (ttt) cc_final: 0.2678 (ttm) REVERT: B 81 MET cc_start: 0.7640 (ppp) cc_final: 0.7235 (ppp) REVERT: C 1 MET cc_start: 0.6123 (mtm) cc_final: 0.5679 (mtp) REVERT: D 1 MET cc_start: 0.7232 (mtm) cc_final: 0.6141 (ttt) REVERT: D 81 MET cc_start: 0.7324 (ppp) cc_final: 0.6667 (ppp) REVERT: E 67 GLU cc_start: 0.8513 (pt0) cc_final: 0.8227 (tp30) REVERT: F 1 MET cc_start: 0.6711 (mtm) cc_final: 0.6239 (ttt) REVERT: F 8 ILE cc_start: 0.8781 (mm) cc_final: 0.8369 (tp) REVERT: F 67 GLU cc_start: 0.8244 (pt0) cc_final: 0.7906 (tp30) REVERT: F 81 MET cc_start: 0.7701 (ppp) cc_final: 0.6790 (ppp) REVERT: G 3 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7266 (tpt-90) REVERT: G 8 ILE cc_start: 0.8916 (mp) cc_final: 0.8351 (tp) REVERT: G 26 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8500 (ttpt) REVERT: G 59 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7969 (t80) REVERT: H 81 MET cc_start: 0.7728 (ppp) cc_final: 0.7276 (ppp) REVERT: I 1 MET cc_start: 0.7163 (mtt) cc_final: 0.5914 (ttt) REVERT: I 8 ILE cc_start: 0.8188 (mp) cc_final: 0.7568 (tp) REVERT: I 67 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6862 (mm-30) REVERT: J 1 MET cc_start: 0.6968 (mtm) cc_final: 0.5229 (ttt) REVERT: J 15 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8371 (pp) REVERT: J 59 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6899 (t80) REVERT: J 81 MET cc_start: 0.6954 (ppp) cc_final: 0.6536 (ppp) REVERT: K 1 MET cc_start: 0.7270 (mtt) cc_final: 0.6563 (ttt) REVERT: K 3 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7250 (tpp-160) REVERT: K 5 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7071 (ptm160) REVERT: L 81 MET cc_start: 0.7215 (ppp) cc_final: 0.6825 (ppp) REVERT: M 81 MET cc_start: 0.7565 (ppp) cc_final: 0.7020 (ppp) REVERT: N 81 MET cc_start: 0.7893 (ppp) cc_final: 0.7161 (ppp) REVERT: O 8 ILE cc_start: 0.9136 (mm) cc_final: 0.8837 (tp) outliers start: 95 outliers final: 78 residues processed: 448 average time/residue: 0.1075 time to fit residues: 65.6225 Evaluate side-chains 466 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 382 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 52 LEU Chi-restraints excluded: chain B residue 59 PHE 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 44 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 30 VAL 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 73 LEU 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 F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 PHE 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 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 54 ASP Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 59 PHE 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 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 51 ASP 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 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 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 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 67 optimal weight: 0.0970 chunk 12 optimal weight: 0.0570 chunk 50 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 3.0100 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.090156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086596 restraints weight = 40062.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088022 restraints weight = 12290.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088805 restraints weight = 5206.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.089257 restraints weight = 2563.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089567 restraints weight = 1463.670| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 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 = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.8409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10695 Z= 0.143 Angle : 0.884 10.170 14385 Z= 0.406 Chirality : 0.043 0.290 1680 Planarity : 0.004 0.046 1860 Dihedral : 6.615 46.627 1518 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 7.85 % Allowed : 38.45 % Favored : 53.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.23), residues: 1335 helix: -1.04 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.55 (0.35), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 74 TYR 0.011 0.002 TYR L 64 PHE 0.013 0.001 PHE D 23 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00330 (10695) covalent geometry : angle 0.88408 (14385) hydrogen bonds : bond 0.04355 ( 475) hydrogen bonds : angle 5.67304 ( 1404) =============================================================================== Job complete usr+sys time: 1814.49 seconds wall clock time: 32 minutes 5.56 seconds (1925.56 seconds total)