Starting phenix.real_space_refine on Fri Feb 14 07:32:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j63_5830/02_2025/3j63_5830.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j63_5830/02_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_5830/02_2025/3j63_5830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j63_5830/02_2025/3j63_5830.map" model { file = "/net/cci-nas-00/data/ceres_data/3j63_5830/02_2025/3j63_5830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j63_5830/02_2025/3j63_5830.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6675 2.51 5 N 1830 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "O" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Residues with excluded nonbonded symmetry interactions: 1365 residue: pdb=" N MET A 1 " occ=0.44 ... (6 atoms not shown) pdb=" CE MET A 1 " occ=0.44 residue: pdb=" N GLY A 2 " occ=0.41 ... (2 atoms not shown) pdb=" O GLY A 2 " occ=0.41 residue: pdb=" N ARG A 3 " occ=0.57 ... (9 atoms not shown) pdb=" NH2 ARG A 3 " occ=0.57 residue: pdb=" N ALA A 4 " occ=0.58 ... (3 atoms not shown) pdb=" CB ALA A 4 " occ=0.58 residue: pdb=" N ARG A 5 " occ=0.78 ... (9 atoms not shown) pdb=" NH2 ARG A 5 " occ=0.78 residue: pdb=" N ASP A 6 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 6 " occ=0.60 residue: pdb=" N ALA A 7 " occ=0.49 ... (3 atoms not shown) pdb=" CB ALA A 7 " occ=0.49 residue: pdb=" N ILE A 8 " occ=0.71 ... (6 atoms not shown) pdb=" CD1 ILE A 8 " occ=0.71 residue: pdb=" N LEU A 9 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 9 " occ=0.80 residue: pdb=" N ASP A 10 " occ=0.58 ... (6 atoms not shown) pdb=" OD2 ASP A 10 " occ=0.58 residue: pdb=" N ALA A 11 " occ=0.51 ... (3 atoms not shown) pdb=" CB ALA A 11 " occ=0.51 residue: pdb=" N LEU A 12 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 12 " occ=0.80 ... (remaining 1353 not shown) Time building chain proxies: 6.20, per 1000 atoms: 0.59 Number of scatterers: 10590 At special positions: 0 Unit cell: (93.96, 96.12, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2025 8.00 N 1830 7.00 C 6675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.3 seconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.828A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.843A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.667A pdb=" N LEU A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.764A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.231A pdb=" N GLY A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.702A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.890A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.589A pdb=" N LEU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.712A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 4.268A pdb=" N GLY B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 removed outlier: 3.547A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.881A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.565A pdb=" N LEU C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.689A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 4.203A pdb=" N GLY C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 9 Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.839A pdb=" N LYS D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.692A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.890A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.782A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.611A pdb=" N GLN D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 removed outlier: 4.106A pdb=" N ASP E 6 " --> pdb=" O GLY E 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.902A pdb=" N LYS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.019A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.663A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 91 removed outlier: 4.218A pdb=" N GLY E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.727A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.519A pdb=" N LEU F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 47 removed outlier: 3.615A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 60 removed outlier: 4.056A pdb=" N LEU F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.856A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 removed outlier: 4.249A pdb=" N GLY F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 4 Processing helix chain 'G' and resid 5 through 10 Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 47 removed outlier: 3.672A pdb=" N LEU G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.802A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.539A pdb=" N GLN G 84 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 removed outlier: 3.705A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 30 removed outlier: 3.943A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 3.568A pdb=" N LEU H 44 " --> pdb=" O PRO H 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 removed outlier: 3.836A pdb=" N LEU H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 76 removed outlier: 3.808A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.636A pdb=" N GLN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.666A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 47 removed outlier: 3.697A pdb=" N LEU I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 60 removed outlier: 4.049A pdb=" N LEU I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.806A pdb=" N GLU I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 removed outlier: 4.366A pdb=" N GLY I 83 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN I 84 " --> pdb=" O GLU I 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 88 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 10 removed outlier: 3.527A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.951A pdb=" N LYS J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.671A pdb=" N LEU J 44 " --> pdb=" O PRO J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 removed outlier: 3.819A pdb=" N LEU J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.763A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 91 removed outlier: 4.227A pdb=" N GLY J 83 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 88 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.959A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.803A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.633A pdb=" N LEU K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 60 removed outlier: 3.883A pdb=" N LEU K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 76 removed outlier: 3.787A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 removed outlier: 4.148A pdb=" N GLY K 83 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN K 84 " --> pdb=" O GLU K 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.853A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.901A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 47 removed outlier: 3.604A pdb=" N LEU L 44 " --> pdb=" O PRO L 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 60 removed outlier: 3.844A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 76 removed outlier: 3.646A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 91 removed outlier: 4.254A pdb=" N GLY L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN L 86 " --> pdb=" O ALA L 82 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 88 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.849A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.008A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU M 28 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 removed outlier: 3.511A pdb=" N LEU M 44 " --> pdb=" O PRO M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 76 removed outlier: 3.755A pdb=" N GLU M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.514A pdb=" N GLN M 84 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA M 88 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 10 removed outlier: 4.074A pdb=" N ASP N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.940A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 76 removed outlier: 3.630A pdb=" N GLU N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 4.295A pdb=" N GLY N 83 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.701A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.002A pdb=" N LYS O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU O 28 " --> pdb=" O LYS O 24 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER O 29 " --> pdb=" O LEU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 47 removed outlier: 3.783A pdb=" N LEU O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 removed outlier: 4.018A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.819A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.630A pdb=" N GLN O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA O 88 " --> pdb=" O GLN O 84 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3570 1.34 - 1.46: 1003 1.46 - 1.57: 6002 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 10695 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 10690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12919 1.86 - 3.72: 1257 3.72 - 5.58: 140 5.58 - 7.44: 56 7.44 - 9.30: 13 Bond angle restraints: 14385 Sorted by residual: angle pdb=" N SER G 29 " pdb=" CA SER G 29 " pdb=" C SER G 29 " ideal model delta sigma weight residual 111.28 119.35 -8.07 1.09e+00 8.42e-01 5.49e+01 angle pdb=" N VAL D 30 " pdb=" CA VAL D 30 " pdb=" C VAL D 30 " ideal model delta sigma weight residual 108.96 117.07 -8.11 1.10e+00 8.26e-01 5.44e+01 angle pdb=" N VAL B 30 " pdb=" CA VAL B 30 " pdb=" C VAL B 30 " ideal model delta sigma weight residual 108.96 116.99 -8.03 1.10e+00 8.26e-01 5.33e+01 angle pdb=" N VAL E 30 " pdb=" CA VAL E 30 " pdb=" C VAL E 30 " ideal model delta sigma weight residual 108.96 116.73 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" N VAL M 30 " pdb=" CA VAL M 30 " pdb=" C VAL M 30 " ideal model delta sigma weight residual 108.96 116.41 -7.45 1.10e+00 8.26e-01 4.59e+01 ... (remaining 14380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5853 17.23 - 34.46: 487 34.46 - 51.69: 136 51.69 - 68.92: 140 68.92 - 86.15: 14 Dihedral angle restraints: 6630 sinusoidal: 2715 harmonic: 3915 Sorted by residual: dihedral pdb=" CB GLU L 80 " pdb=" CG GLU L 80 " pdb=" CD GLU L 80 " pdb=" OE1 GLU L 80 " ideal model delta sinusoidal sigma weight residual 0.00 86.15 -86.15 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" N LEU D 61 " pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sinusoidal sigma weight residual -180.00 -120.71 -59.29 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET O 1 " pdb=" CG MET O 1 " pdb=" SD MET O 1 " pdb=" CE MET O 1 " ideal model delta sinusoidal sigma weight residual -180.00 -120.73 -59.27 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 729 0.045 - 0.090: 595 0.090 - 0.135: 264 0.135 - 0.179: 78 0.179 - 0.224: 14 Chirality restraints: 1680 Sorted by residual: chirality pdb=" CA SER C 29 " pdb=" N SER C 29 " pdb=" C SER C 29 " pdb=" CB SER C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA SER L 29 " pdb=" N SER L 29 " pdb=" C SER L 29 " pdb=" CB SER L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA SER G 29 " pdb=" N SER G 29 " pdb=" C SER G 29 " pdb=" CB SER G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1677 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 36 " 0.028 2.00e-02 2.50e+03 1.41e-02 3.98e+00 pdb=" CG TYR O 36 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 36 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR O 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 30 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO O 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO O 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO O 31 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 30 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO M 31 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 31 " 0.023 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 979 2.73 - 3.27: 12830 3.27 - 3.81: 17234 3.81 - 4.36: 20542 4.36 - 4.90: 31132 Nonbonded interactions: 82717 Sorted by model distance: nonbonded pdb=" O VAL M 57 " pdb=" O TYR M 60 " model vdw 2.184 3.040 nonbonded pdb=" O LEU M 50 " pdb=" OG1 THR M 53 " model vdw 2.281 3.040 nonbonded pdb=" O LEU H 50 " pdb=" OG1 THR H 53 " model vdw 2.286 3.040 nonbonded pdb=" O LEU A 50 " pdb=" OG1 THR A 53 " model vdw 2.290 3.040 nonbonded pdb=" O LEU J 50 " pdb=" OG1 THR J 53 " model vdw 2.293 3.040 ... (remaining 82712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=0.99 mean=0.64 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 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: 0.410 Check model and map are aligned: 0.000 Set scattering table: 0.100 Process input model: 25.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.540 ------------------------------------------------------------------------------- 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= 0.295 Angle : 1.252 9.305 14385 Z= 0.876 Chirality : 0.072 0.224 1680 Planarity : 0.004 0.042 1860 Dihedral : 17.395 86.154 4110 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 54.83 Ramachandran Plot: Outliers : 3.07 % Allowed : 10.26 % Favored : 86.67 % Rotamer: Outliers : 7.31 % Allowed : 15.25 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.19), residues: 1335 helix: -4.38 (0.12), residues: 510 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 90 PHE 0.008 0.002 PHE B 23 TYR 0.028 0.004 TYR O 36 ARG 0.006 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 519 time to evaluate : 1.214 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: 0.2449 time to fit residues: 184.6973 Evaluate side-chains 407 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain O residue 34 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 14 ASN E 14 ASN F 14 ASN G 14 ASN G 71 ASN J 14 ASN K 14 ASN L 14 ASN N 14 ASN O 14 ASN O 90 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110244 restraints weight = 33780.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112309 restraints weight = 15644.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113618 restraints weight = 8703.198| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 0.99 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10695 Z= 0.239 Angle : 0.878 10.102 14385 Z= 0.429 Chirality : 0.041 0.189 1680 Planarity : 0.006 0.071 1860 Dihedral : 9.159 58.334 1595 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.76 % Allowed : 28.22 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.21), residues: 1335 helix: -2.17 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.46 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 90 PHE 0.029 0.003 PHE B 59 TYR 0.022 0.002 TYR G 64 ARG 0.004 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 1.632 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: 0.6643 (mtm) cc_final: 0.6432 (ttt) REVERT: B 1 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5544 (ttt) REVERT: C 1 MET cc_start: 0.7180 (mtm) cc_final: 0.6056 (ttp) REVERT: C 26 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8123 (ttpp) REVERT: C 39 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8363 (mt) REVERT: D 1 MET cc_start: 0.7631 (mtm) cc_final: 0.6256 (ttt) REVERT: D 9 LEU cc_start: 0.8669 (tp) cc_final: 0.8456 (tp) REVERT: E 8 ILE cc_start: 0.8636 (mm) cc_final: 0.8263 (tp) REVERT: F 1 MET cc_start: 0.7403 (mtm) cc_final: 0.6070 (ttt) REVERT: F 51 ASP cc_start: 0.8347 (m-30) cc_final: 0.8050 (m-30) REVERT: F 58 SER cc_start: 0.8529 (m) cc_final: 0.8259 (p) REVERT: H 8 ILE cc_start: 0.9185 (mm) cc_final: 0.8943 (tp) REVERT: H 38 ARG cc_start: 0.6860 (mtt180) cc_final: 0.6558 (mtt180) REVERT: H 73 LEU cc_start: 0.8678 (mt) cc_final: 0.8035 (tp) REVERT: I 1 MET cc_start: 0.7451 (mtt) cc_final: 0.5411 (ttt) REVERT: I 67 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6846 (mm-30) REVERT: J 1 MET cc_start: 0.7774 (mtm) cc_final: 0.5606 (ttt) REVERT: J 79 GLN cc_start: 0.6323 (mp10) cc_final: 0.6000 (mp10) REVERT: K 1 MET cc_start: 0.7415 (mtt) cc_final: 0.6296 (ttm) REVERT: K 5 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7470 (ptm160) REVERT: K 51 ASP cc_start: 0.7996 (m-30) cc_final: 0.7576 (m-30) REVERT: L 50 LEU cc_start: 0.8429 (mt) cc_final: 0.8195 (mt) REVERT: M 6 ASP cc_start: 0.8307 (t70) cc_final: 0.8081 (t0) REVERT: M 51 ASP cc_start: 0.8765 (m-30) cc_final: 0.8486 (m-30) REVERT: O 1 MET cc_start: 0.7941 (mtt) cc_final: 0.6728 (ttt) REVERT: O 8 ILE cc_start: 0.9242 (mm) cc_final: 0.8778 (tp) REVERT: O 24 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8678 (mtpp) REVERT: O 26 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8073 (ttpt) REVERT: O 51 ASP cc_start: 0.7610 (m-30) cc_final: 0.6815 (m-30) outliers start: 74 outliers final: 42 residues processed: 479 average time/residue: 0.2574 time to fit residues: 165.3546 Evaluate side-chains 418 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 373 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 94 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 40.0000 chunk 133 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093839 restraints weight = 38969.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095575 restraints weight = 15290.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096738 restraints weight = 7843.724| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10695 Z= 0.233 Angle : 0.807 7.315 14385 Z= 0.386 Chirality : 0.041 0.230 1680 Planarity : 0.005 0.059 1860 Dihedral : 7.509 58.814 1523 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 11.05 % Allowed : 28.40 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1335 helix: -1.47 (0.15), residues: 825 sheet: None (None), residues: 0 loop : 0.24 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.011 0.002 PHE B 59 TYR 0.015 0.002 TYR O 64 ARG 0.005 0.000 ARG A 33 *********************** 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 522 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 401 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7125 (mtm) cc_final: 0.6524 (ttt) REVERT: B 1 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5743 (ttt) REVERT: B 26 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8473 (ttpt) REVERT: C 1 MET cc_start: 0.6281 (mtm) cc_final: 0.5669 (mtp) REVERT: C 39 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8727 (mt) REVERT: D 1 MET cc_start: 0.7357 (mtm) cc_final: 0.5867 (ttt) REVERT: E 8 ILE cc_start: 0.8728 (mm) cc_final: 0.8405 (tp) REVERT: E 76 MET cc_start: 0.5227 (ttt) cc_final: 0.4866 (ttp) REVERT: F 1 MET cc_start: 0.6886 (mtm) cc_final: 0.5969 (ttt) REVERT: F 8 ILE cc_start: 0.8891 (mm) cc_final: 0.8501 (tp) REVERT: F 20 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8230 (tm) REVERT: F 51 ASP cc_start: 0.7845 (m-30) cc_final: 0.7388 (m-30) REVERT: H 8 ILE cc_start: 0.9275 (mm) cc_final: 0.9062 (tp) REVERT: I 1 MET cc_start: 0.7156 (mtt) cc_final: 0.5577 (ttt) REVERT: I 39 ILE cc_start: 0.9096 (mp) cc_final: 0.8703 (mm) REVERT: I 67 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6604 (mm-30) REVERT: J 1 MET cc_start: 0.7641 (mtm) cc_final: 0.5469 (ttt) REVERT: J 51 ASP cc_start: 0.7643 (m-30) cc_final: 0.7120 (m-30) REVERT: K 1 MET cc_start: 0.7257 (mtt) cc_final: 0.6114 (ttm) REVERT: K 5 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7379 (ptm160) REVERT: K 51 ASP cc_start: 0.8016 (m-30) cc_final: 0.7799 (m-30) REVERT: L 73 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8483 (mt) REVERT: M 39 ILE cc_start: 0.8839 (mp) cc_final: 0.8559 (mm) REVERT: O 1 MET cc_start: 0.7590 (mtt) cc_final: 0.6082 (ttt) REVERT: O 8 ILE cc_start: 0.9203 (mm) cc_final: 0.8809 (tp) REVERT: O 26 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8033 (ttpt) REVERT: O 51 ASP cc_start: 0.8293 (m-30) cc_final: 0.7871 (m-30) outliers start: 121 outliers final: 85 residues processed: 466 average time/residue: 0.2516 time to fit residues: 158.0333 Evaluate side-chains 458 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 367 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 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 26 LYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 10 optimal weight: 0.0570 chunk 37 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.093243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088245 restraints weight = 38428.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089940 restraints weight = 14288.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090995 restraints weight = 6862.793| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10695 Z= 0.215 Angle : 0.753 7.276 14385 Z= 0.361 Chirality : 0.039 0.197 1680 Planarity : 0.005 0.059 1860 Dihedral : 7.217 56.133 1521 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 12.88 % Allowed : 28.86 % Favored : 58.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1335 helix: -1.24 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.10 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.009 0.002 PHE A 59 TYR 0.013 0.002 TYR J 64 ARG 0.004 0.000 ARG N 5 *********************** 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 545 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 404 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6901 (mtm) cc_final: 0.6286 (ttt) REVERT: B 20 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8819 (tm) REVERT: C 1 MET cc_start: 0.6224 (mtm) cc_final: 0.5527 (mtp) REVERT: D 1 MET cc_start: 0.7718 (mtm) cc_final: 0.5993 (ttt) REVERT: E 8 ILE cc_start: 0.8679 (mm) cc_final: 0.8421 (tp) REVERT: E 76 MET cc_start: 0.5092 (ttt) cc_final: 0.4714 (ttp) REVERT: F 1 MET cc_start: 0.7061 (mtm) cc_final: 0.5968 (ttt) REVERT: F 8 ILE cc_start: 0.8829 (mm) cc_final: 0.8446 (tp) REVERT: F 20 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8489 (tm) REVERT: F 51 ASP cc_start: 0.7860 (m-30) cc_final: 0.7312 (m-30) REVERT: G 26 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8232 (ttpt) REVERT: G 59 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8189 (t80) REVERT: H 8 ILE cc_start: 0.9268 (mm) cc_final: 0.9005 (tp) REVERT: H 81 MET cc_start: 0.7621 (ppp) cc_final: 0.6925 (ppp) REVERT: I 1 MET cc_start: 0.7334 (mtt) cc_final: 0.5933 (ttt) REVERT: I 67 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6616 (mm-30) REVERT: J 1 MET cc_start: 0.7366 (mtm) cc_final: 0.5437 (ttt) REVERT: J 51 ASP cc_start: 0.7726 (m-30) cc_final: 0.7327 (m-30) REVERT: K 1 MET cc_start: 0.6950 (mtt) cc_final: 0.6119 (ttt) REVERT: K 5 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7329 (ptm160) REVERT: K 50 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8177 (mt) REVERT: K 75 ASP cc_start: 0.7155 (m-30) cc_final: 0.6764 (m-30) REVERT: L 25 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8762 (tt) REVERT: L 39 ILE cc_start: 0.9182 (mp) cc_final: 0.8971 (mm) REVERT: L 50 LEU cc_start: 0.8179 (mt) cc_final: 0.7945 (mp) REVERT: L 81 MET cc_start: 0.7572 (ppp) cc_final: 0.7156 (ppp) REVERT: O 1 MET cc_start: 0.7524 (mtt) cc_final: 0.6129 (ttt) REVERT: O 8 ILE cc_start: 0.9183 (mm) cc_final: 0.8815 (tp) REVERT: O 20 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8131 (tm) REVERT: O 51 ASP cc_start: 0.8163 (m-30) cc_final: 0.7726 (m-30) outliers start: 141 outliers final: 95 residues processed: 486 average time/residue: 0.2448 time to fit residues: 160.5786 Evaluate side-chains 475 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 373 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 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 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain 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 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 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 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 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain 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 25 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP 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 20 LEU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.089754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085368 restraints weight = 38976.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086917 restraints weight = 13337.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087865 restraints weight = 6044.443| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6822 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= 0.269 Angle : 0.801 8.475 14385 Z= 0.381 Chirality : 0.041 0.180 1680 Planarity : 0.005 0.053 1860 Dihedral : 7.167 57.377 1518 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 13.61 % Allowed : 28.95 % Favored : 57.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1335 helix: -1.36 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.38 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 90 PHE 0.015 0.002 PHE I 59 TYR 0.035 0.002 TYR J 64 ARG 0.006 0.001 ARG D 74 *********************** 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 548 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 399 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7064 (mtm) cc_final: 0.6239 (ttt) REVERT: A 81 MET cc_start: 0.7472 (ppp) cc_final: 0.7155 (ppp) REVERT: B 20 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8812 (tm) REVERT: C 1 MET cc_start: 0.6156 (mtm) cc_final: 0.5442 (mtp) REVERT: C 15 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7989 (pp) REVERT: C 51 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8595 (m-30) REVERT: D 1 MET cc_start: 0.7228 (mtm) cc_final: 0.6277 (ttt) REVERT: E 8 ILE cc_start: 0.8389 (mm) cc_final: 0.8132 (tp) REVERT: E 76 MET cc_start: 0.5006 (ttt) cc_final: 0.4670 (ttp) REVERT: F 1 MET cc_start: 0.6805 (mtm) cc_final: 0.6246 (ttt) REVERT: F 8 ILE cc_start: 0.8865 (mm) cc_final: 0.8481 (tp) REVERT: F 51 ASP cc_start: 0.7963 (m-30) cc_final: 0.7708 (m-30) REVERT: G 8 ILE cc_start: 0.8733 (mm) cc_final: 0.8423 (tp) REVERT: G 26 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8393 (ttpt) REVERT: G 39 ILE cc_start: 0.8804 (mp) cc_final: 0.8459 (mm) REVERT: G 59 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8250 (t80) REVERT: H 8 ILE cc_start: 0.9268 (mm) cc_final: 0.9022 (tp) REVERT: H 81 MET cc_start: 0.7622 (ppp) cc_final: 0.7005 (ppp) REVERT: I 1 MET cc_start: 0.7179 (mtt) cc_final: 0.5829 (ttt) REVERT: I 67 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6833 (mm-30) REVERT: J 1 MET cc_start: 0.7238 (mtm) cc_final: 0.5371 (ttt) REVERT: J 22 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: J 81 MET cc_start: 0.7385 (ppp) cc_final: 0.7139 (ppp) REVERT: K 1 MET cc_start: 0.7002 (mtt) cc_final: 0.6618 (ttt) REVERT: K 5 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7388 (ptm160) REVERT: K 50 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8020 (mt) REVERT: L 25 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8853 (tt) REVERT: L 39 ILE cc_start: 0.9058 (mp) cc_final: 0.8804 (mm) REVERT: L 81 MET cc_start: 0.7411 (ppp) cc_final: 0.6621 (ppp) REVERT: M 39 ILE cc_start: 0.8896 (mp) cc_final: 0.8660 (mm) REVERT: M 48 ASP cc_start: 0.7689 (t0) cc_final: 0.7484 (t0) REVERT: O 8 ILE cc_start: 0.9148 (mm) cc_final: 0.8815 (tp) REVERT: O 20 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (tm) REVERT: O 67 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7038 (pm20) outliers start: 149 outliers final: 102 residues processed: 490 average time/residue: 0.2473 time to fit residues: 164.9030 Evaluate side-chains 483 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 372 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 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 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 22 LYS 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 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 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 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 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN H 91 GLN N 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085459 restraints weight = 38507.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086897 restraints weight = 12292.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087773 restraints weight = 5408.895| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 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 = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10695 Z= 0.232 Angle : 0.795 7.912 14385 Z= 0.376 Chirality : 0.042 0.206 1680 Planarity : 0.005 0.076 1860 Dihedral : 7.050 58.848 1518 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 12.60 % Allowed : 32.60 % Favored : 54.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1335 helix: -1.24 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.53 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.010 0.002 PHE E 59 TYR 0.028 0.002 TYR B 64 ARG 0.005 0.000 ARG D 74 *********************** 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 545 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 407 time to evaluate : 1.296 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: 0.7121 (mtm) cc_final: 0.6477 (ttt) REVERT: A 81 MET cc_start: 0.7564 (ppp) cc_final: 0.7253 (ppp) REVERT: B 20 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8837 (tm) REVERT: C 1 MET cc_start: 0.6109 (mtm) cc_final: 0.5682 (mtp) REVERT: C 15 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8002 (pp) REVERT: D 1 MET cc_start: 0.7338 (mtm) cc_final: 0.6302 (ttt) REVERT: E 8 ILE cc_start: 0.8437 (mm) cc_final: 0.8173 (tp) REVERT: E 76 MET cc_start: 0.4845 (ttt) cc_final: 0.4619 (ttt) REVERT: F 1 MET cc_start: 0.6750 (mtm) cc_final: 0.6154 (ttt) REVERT: F 8 ILE cc_start: 0.8892 (mm) cc_final: 0.8482 (tp) REVERT: F 81 MET cc_start: 0.7434 (ppp) cc_final: 0.6940 (ppp) REVERT: G 26 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8394 (ttpt) REVERT: G 59 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8116 (t80) REVERT: H 8 ILE cc_start: 0.9278 (mm) cc_final: 0.9009 (tp) REVERT: H 81 MET cc_start: 0.7774 (ppp) cc_final: 0.7197 (ppp) REVERT: I 1 MET cc_start: 0.6930 (mtt) cc_final: 0.5834 (ttt) REVERT: I 67 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6752 (mm-30) REVERT: J 1 MET cc_start: 0.7160 (mtm) cc_final: 0.5333 (ttt) REVERT: J 75 ASP cc_start: 0.7497 (t0) cc_final: 0.7089 (p0) REVERT: K 1 MET cc_start: 0.7151 (mtt) cc_final: 0.6572 (ttt) REVERT: K 3 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6016 (tmt170) REVERT: K 5 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7325 (ptm160) REVERT: K 50 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7964 (mt) REVERT: L 25 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8911 (tt) REVERT: L 39 ILE cc_start: 0.9072 (mp) cc_final: 0.8795 (mm) REVERT: L 81 MET cc_start: 0.7380 (ppp) cc_final: 0.6694 (ppp) REVERT: M 1 MET cc_start: 0.4290 (ttt) cc_final: 0.3440 (ttm) REVERT: M 26 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8459 (ttpt) REVERT: M 39 ILE cc_start: 0.8870 (mp) cc_final: 0.8599 (mm) REVERT: M 48 ASP cc_start: 0.7784 (t0) cc_final: 0.7553 (t0) REVERT: M 81 MET cc_start: 0.7939 (ppp) cc_final: 0.7623 (ppp) REVERT: O 8 ILE cc_start: 0.9139 (mm) cc_final: 0.8829 (tp) REVERT: O 24 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8462 (mtmt) REVERT: O 51 ASP cc_start: 0.8363 (m-30) cc_final: 0.8120 (m-30) outliers start: 138 outliers final: 100 residues processed: 493 average time/residue: 0.2549 time to fit residues: 170.4736 Evaluate side-chains 491 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 384 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 53 THR Chi-restraints excluded: chain A residue 76 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 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 15 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain 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 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 5 ARG 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 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE 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 102 optimal weight: 0.0050 chunk 52 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087164 restraints weight = 39582.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088741 restraints weight = 13034.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089641 restraints weight = 5795.623| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 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 = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10695 Z= 0.198 Angle : 0.794 9.497 14385 Z= 0.369 Chirality : 0.041 0.181 1680 Planarity : 0.005 0.057 1860 Dihedral : 6.890 58.598 1518 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 10.23 % Allowed : 36.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1335 helix: -1.02 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.42 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 90 PHE 0.012 0.001 PHE D 23 TYR 0.021 0.002 TYR J 64 ARG 0.009 0.000 ARG B 74 *********************** 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 522 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 410 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7016 (mtm) cc_final: 0.5421 (ttt) REVERT: A 8 ILE cc_start: 0.8692 (mm) cc_final: 0.7872 (tp) REVERT: C 1 MET cc_start: 0.6084 (mtm) cc_final: 0.5641 (mtp) REVERT: C 15 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8042 (pp) REVERT: C 52 LEU cc_start: 0.8719 (tp) cc_final: 0.8222 (tp) REVERT: D 1 MET cc_start: 0.7103 (mtm) cc_final: 0.5974 (ttt) REVERT: E 8 ILE cc_start: 0.8467 (mm) cc_final: 0.8237 (tp) REVERT: F 1 MET cc_start: 0.6803 (mtm) cc_final: 0.6199 (ttt) REVERT: F 8 ILE cc_start: 0.8870 (mm) cc_final: 0.8471 (tp) REVERT: F 81 MET cc_start: 0.7113 (ppp) cc_final: 0.6849 (ppp) REVERT: G 8 ILE cc_start: 0.8724 (mp) cc_final: 0.8102 (tp) REVERT: G 26 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8517 (ttpt) REVERT: G 59 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7917 (t80) REVERT: H 8 ILE cc_start: 0.9228 (mm) cc_final: 0.8984 (tp) REVERT: H 81 MET cc_start: 0.7720 (ppp) cc_final: 0.7234 (ppp) REVERT: I 1 MET cc_start: 0.6914 (mtt) cc_final: 0.5849 (ttt) REVERT: I 8 ILE cc_start: 0.8576 (mm) cc_final: 0.8068 (tp) REVERT: I 67 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6802 (mm-30) REVERT: J 1 MET cc_start: 0.7012 (mtm) cc_final: 0.5178 (ttt) REVERT: J 81 MET cc_start: 0.7215 (ppp) cc_final: 0.6569 (ppp) REVERT: K 1 MET cc_start: 0.7257 (mtt) cc_final: 0.6577 (ttt) REVERT: K 50 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7997 (mt) REVERT: L 39 ILE cc_start: 0.9003 (mp) cc_final: 0.8730 (mm) REVERT: L 81 MET cc_start: 0.7398 (ppp) cc_final: 0.6797 (ppp) REVERT: M 1 MET cc_start: 0.4075 (ttt) cc_final: 0.3189 (ttm) REVERT: M 26 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8440 (ttpt) REVERT: M 39 ILE cc_start: 0.8764 (mp) cc_final: 0.8495 (mm) REVERT: M 81 MET cc_start: 0.7857 (ppp) cc_final: 0.7429 (ppp) REVERT: N 81 MET cc_start: 0.7896 (ppp) cc_final: 0.7203 (ppp) REVERT: O 8 ILE cc_start: 0.9220 (mm) cc_final: 0.8952 (tp) outliers start: 112 outliers final: 79 residues processed: 472 average time/residue: 0.2461 time to fit residues: 157.1525 Evaluate side-chains 473 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 391 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 59 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 9 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 C residue 5 ARG Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 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 73 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 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 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 73 LEU Chi-restraints excluded: chain J residue 9 LEU 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 5 ARG 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 L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP 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 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 73 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 20 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 130 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 61 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 102 optimal weight: 0.0020 chunk 0 optimal weight: 40.0000 overall best weight: 2.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087878 restraints weight = 39683.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089451 restraints weight = 12870.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090363 restraints weight = 5648.027| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7786 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= 0.204 Angle : 0.837 12.948 14385 Z= 0.386 Chirality : 0.042 0.223 1680 Planarity : 0.005 0.049 1860 Dihedral : 6.680 59.840 1516 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 9.50 % Allowed : 37.17 % Favored : 53.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1335 helix: -1.01 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.43 (0.35), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 90 PHE 0.008 0.002 PHE K 59 TYR 0.018 0.001 TYR J 64 ARG 0.006 0.000 ARG B 74 *********************** 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 521 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 417 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6950 (mtm) cc_final: 0.5451 (ttt) REVERT: A 8 ILE cc_start: 0.8781 (mm) cc_final: 0.8064 (tp) REVERT: C 1 MET cc_start: 0.6162 (mtm) cc_final: 0.5698 (mtp) REVERT: C 15 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8163 (pp) REVERT: C 53 THR cc_start: 0.8136 (t) cc_final: 0.7651 (t) REVERT: D 1 MET cc_start: 0.7144 (mtm) cc_final: 0.6580 (ttt) REVERT: D 81 MET cc_start: 0.7694 (ppp) cc_final: 0.7332 (ppp) REVERT: E 8 ILE cc_start: 0.8635 (mm) cc_final: 0.8372 (tp) REVERT: E 39 ILE cc_start: 0.8944 (mp) cc_final: 0.8695 (mm) REVERT: F 1 MET cc_start: 0.6676 (mtm) cc_final: 0.6072 (ttt) REVERT: F 8 ILE cc_start: 0.8845 (mm) cc_final: 0.8473 (tp) REVERT: F 26 LYS cc_start: 0.8024 (tptt) cc_final: 0.7774 (ttpt) REVERT: F 81 MET cc_start: 0.7098 (ppp) cc_final: 0.6885 (ppp) REVERT: G 8 ILE cc_start: 0.8754 (mp) cc_final: 0.8158 (tp) REVERT: G 26 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8344 (ttpt) REVERT: G 59 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8041 (t80) REVERT: H 8 ILE cc_start: 0.9219 (mm) cc_final: 0.8957 (tp) REVERT: H 81 MET cc_start: 0.7674 (ppp) cc_final: 0.7299 (ppp) REVERT: I 1 MET cc_start: 0.6927 (mtt) cc_final: 0.5781 (ttt) REVERT: I 8 ILE cc_start: 0.8606 (mm) cc_final: 0.8117 (tp) REVERT: I 67 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6797 (mm-30) REVERT: J 1 MET cc_start: 0.7157 (mtm) cc_final: 0.5271 (ttt) REVERT: J 10 ASP cc_start: 0.9471 (m-30) cc_final: 0.9232 (m-30) REVERT: J 81 MET cc_start: 0.6992 (ppp) cc_final: 0.6485 (ppp) REVERT: K 1 MET cc_start: 0.7349 (mtt) cc_final: 0.6611 (ttt) REVERT: K 5 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7222 (ptm160) REVERT: L 81 MET cc_start: 0.7194 (ppp) cc_final: 0.6724 (ppp) REVERT: M 1 MET cc_start: 0.3973 (ttt) cc_final: 0.3116 (ttm) REVERT: M 20 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (tm) REVERT: M 26 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8477 (ttpt) REVERT: M 39 ILE cc_start: 0.8801 (mp) cc_final: 0.8475 (mm) REVERT: M 81 MET cc_start: 0.7698 (ppp) cc_final: 0.7097 (ppp) REVERT: N 81 MET cc_start: 0.7934 (ppp) cc_final: 0.7233 (ppp) REVERT: O 8 ILE cc_start: 0.9198 (mm) cc_final: 0.8921 (tp) REVERT: O 24 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8761 (ptmt) outliers start: 104 outliers final: 85 residues processed: 475 average time/residue: 0.2561 time to fit residues: 164.2956 Evaluate side-chains 488 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 398 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 15 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 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 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 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 73 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 56 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 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 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR 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 16 THR Chi-restraints excluded: chain L residue 20 LEU 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 3 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090178 restraints weight = 39604.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091721 restraints weight = 12125.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092576 restraints weight = 5111.215| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10695 Z= 0.203 Angle : 0.864 14.255 14385 Z= 0.393 Chirality : 0.042 0.246 1680 Planarity : 0.004 0.046 1860 Dihedral : 6.614 58.985 1516 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 7.12 % Allowed : 39.63 % Favored : 53.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1335 helix: -1.12 (0.16), residues: 900 sheet: None (None), residues: 0 loop : 1.69 (0.36), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.010 0.001 PHE K 59 TYR 0.017 0.001 TYR B 64 ARG 0.006 0.000 ARG B 74 *********************** 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 510 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 432 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6893 (mtm) cc_final: 0.6114 (ttt) REVERT: A 8 ILE cc_start: 0.8853 (mm) cc_final: 0.8179 (tp) REVERT: C 1 MET cc_start: 0.6160 (mtm) cc_final: 0.4056 (ttt) REVERT: C 15 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8221 (pp) REVERT: D 1 MET cc_start: 0.7025 (mtm) cc_final: 0.6487 (ttt) REVERT: D 81 MET cc_start: 0.7430 (ppp) cc_final: 0.7114 (ppp) REVERT: E 8 ILE cc_start: 0.8560 (mm) cc_final: 0.8257 (tp) REVERT: E 39 ILE cc_start: 0.8913 (mp) cc_final: 0.8713 (mm) REVERT: E 67 GLU cc_start: 0.8638 (pt0) cc_final: 0.8103 (tp30) REVERT: F 1 MET cc_start: 0.6771 (mtm) cc_final: 0.6152 (ttt) REVERT: F 8 ILE cc_start: 0.8882 (mm) cc_final: 0.8491 (tp) REVERT: F 26 LYS cc_start: 0.8067 (tptt) cc_final: 0.7664 (ttpt) REVERT: F 34 GLU cc_start: 0.5948 (pm20) cc_final: 0.4906 (tm-30) REVERT: G 8 ILE cc_start: 0.8725 (mp) cc_final: 0.8147 (tp) REVERT: G 26 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8251 (ttpt) REVERT: G 59 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7927 (t80) REVERT: H 8 ILE cc_start: 0.9184 (mm) cc_final: 0.8917 (tp) REVERT: H 81 MET cc_start: 0.7453 (ppp) cc_final: 0.7020 (ppp) REVERT: I 1 MET cc_start: 0.6975 (mtt) cc_final: 0.5755 (ttt) REVERT: I 8 ILE cc_start: 0.8598 (mm) cc_final: 0.8118 (tp) REVERT: I 67 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6592 (mm-30) REVERT: J 1 MET cc_start: 0.6774 (mtm) cc_final: 0.5037 (ttt) REVERT: J 10 ASP cc_start: 0.9433 (m-30) cc_final: 0.9207 (m-30) REVERT: J 22 LYS cc_start: 0.8317 (mmmm) cc_final: 0.7981 (mmtp) REVERT: J 81 MET cc_start: 0.6919 (ppp) cc_final: 0.6677 (ppp) REVERT: K 1 MET cc_start: 0.7312 (mtt) cc_final: 0.6586 (ttt) REVERT: K 6 ASP cc_start: 0.8917 (t0) cc_final: 0.8500 (t0) REVERT: L 81 MET cc_start: 0.7287 (ppp) cc_final: 0.6912 (ppp) REVERT: M 1 MET cc_start: 0.3802 (ttt) cc_final: 0.2872 (ttm) REVERT: M 20 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (tm) REVERT: M 81 MET cc_start: 0.7386 (ppp) cc_final: 0.6898 (ppp) REVERT: N 81 MET cc_start: 0.7850 (ppp) cc_final: 0.7145 (ppp) REVERT: O 8 ILE cc_start: 0.9199 (mm) cc_final: 0.8863 (tp) REVERT: O 24 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8704 (ptmt) outliers start: 78 outliers final: 48 residues processed: 477 average time/residue: 0.2548 time to fit residues: 162.8487 Evaluate side-chains 444 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 393 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 28 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 53 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain 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 H residue 16 THR Chi-restraints excluded: chain H residue 59 PHE 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 J residue 9 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 chunk 7 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085804 restraints weight = 38803.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087439 restraints weight = 13486.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.088362 restraints weight = 6080.687| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10695 Z= 0.285 Angle : 0.949 12.272 14385 Z= 0.445 Chirality : 0.045 0.251 1680 Planarity : 0.005 0.051 1860 Dihedral : 6.548 50.855 1514 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 7.40 % Allowed : 40.18 % Favored : 52.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1335 helix: -1.15 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.28 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 90 PHE 0.014 0.002 PHE O 59 TYR 0.025 0.002 TYR J 64 ARG 0.010 0.001 ARG E 74 ********************** 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 463 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 382 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6711 (mtm) cc_final: 0.5268 (ttt) REVERT: B 1 MET cc_start: 0.3621 (ttt) cc_final: 0.3029 (ttm) REVERT: C 1 MET cc_start: 0.6110 (mtm) cc_final: 0.4045 (ttt) REVERT: C 15 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 50 LEU cc_start: 0.8203 (mp) cc_final: 0.7975 (mp) REVERT: D 1 MET cc_start: 0.7153 (mtm) cc_final: 0.6565 (ttt) REVERT: D 81 MET cc_start: 0.7394 (ppp) cc_final: 0.7016 (ppp) REVERT: E 8 ILE cc_start: 0.8627 (mm) cc_final: 0.8366 (tp) REVERT: F 1 MET cc_start: 0.6710 (mtm) cc_final: 0.6107 (ttt) REVERT: F 8 ILE cc_start: 0.8915 (mm) cc_final: 0.8512 (tp) REVERT: F 26 LYS cc_start: 0.8046 (tptt) cc_final: 0.7640 (ttpt) REVERT: G 8 ILE cc_start: 0.8704 (mp) cc_final: 0.8133 (tp) REVERT: G 26 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8368 (ttpt) REVERT: G 59 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8179 (t80) REVERT: H 8 ILE cc_start: 0.9163 (mm) cc_final: 0.8879 (tp) REVERT: H 81 MET cc_start: 0.7372 (ppp) cc_final: 0.7044 (ppp) REVERT: I 1 MET cc_start: 0.7113 (mtt) cc_final: 0.5896 (ttt) REVERT: I 47 MET cc_start: 0.7201 (tpp) cc_final: 0.6958 (tpp) REVERT: I 59 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6817 (t80) REVERT: I 67 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6798 (mm-30) REVERT: J 1 MET cc_start: 0.7060 (mtm) cc_final: 0.5278 (ttt) REVERT: J 10 ASP cc_start: 0.9434 (m-30) cc_final: 0.9189 (m-30) REVERT: J 59 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6930 (t80) REVERT: J 75 ASP cc_start: 0.7596 (t0) cc_final: 0.7152 (p0) REVERT: J 81 MET cc_start: 0.6947 (ppp) cc_final: 0.6609 (ppp) REVERT: K 1 MET cc_start: 0.7241 (mtt) cc_final: 0.6589 (ttt) REVERT: K 3 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7103 (tpp-160) REVERT: K 5 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7183 (ptm160) REVERT: L 22 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8637 (tptt) REVERT: L 81 MET cc_start: 0.7381 (ppp) cc_final: 0.6970 (ppp) REVERT: M 8 ILE cc_start: 0.9155 (mp) cc_final: 0.8838 (mp) REVERT: M 20 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (tm) REVERT: M 76 MET cc_start: 0.4881 (ttt) cc_final: 0.2863 (ttt) REVERT: M 81 MET cc_start: 0.7842 (ppp) cc_final: 0.7330 (ppp) REVERT: N 81 MET cc_start: 0.8022 (ppp) cc_final: 0.7407 (ppp) REVERT: O 8 ILE cc_start: 0.9208 (mm) cc_final: 0.8908 (tp) REVERT: O 24 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8875 (ptmt) REVERT: O 75 ASP cc_start: 0.8644 (t0) cc_final: 0.8071 (m-30) outliers start: 81 outliers final: 69 residues processed: 429 average time/residue: 0.2549 time to fit residues: 147.4024 Evaluate side-chains 444 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 368 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 50 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 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 19 GLU 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 73 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 28 LEU 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 54 ASP Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain J residue 9 LEU 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 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain 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 59 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 85 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 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 125 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.090562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086372 restraints weight = 39354.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087887 restraints weight = 13245.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088777 restraints weight = 6051.087| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10695 Z= 0.239 Angle : 0.936 12.439 14385 Z= 0.433 Chirality : 0.044 0.249 1680 Planarity : 0.005 0.049 1860 Dihedral : 6.519 50.447 1514 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 7.40 % Allowed : 41.00 % Favored : 51.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1335 helix: -1.17 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.23 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.009 0.002 PHE B 59 TYR 0.019 0.002 TYR J 64 ARG 0.008 0.001 ARG E 74 =============================================================================== Job complete usr+sys time: 3573.55 seconds wall clock time: 64 minutes 42.41 seconds (3882.41 seconds total)