Starting phenix.real_space_refine on Thu Mar 5 05:17:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq9_33391/03_2026/7xq9_33391.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.175 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 96 5.16 5 C 13080 2.51 5 N 3120 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19632 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Restraints were copied for chains: G, B, C, D, E, F, H, I, J, K, L Time building chain proxies: 2.02, per 1000 atoms: 0.10 Number of scatterers: 19632 At special positions: 0 Unit cell: (106.392, 108.68, 181.896, 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 96 16.00 O 3336 8.00 N 3120 7.00 C 13080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 958.9 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N LYS A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 110 Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N LYS G 102 " --> pdb=" O TYR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.658A pdb=" N TYR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 236 " --> pdb=" O PHE G 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix removed outlier: 3.584A pdb=" N LYS B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix removed outlier: 3.584A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix removed outlier: 3.584A pdb=" N LYS D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N LYS E 102 " --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N LYS F 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.700A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 45' Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 110 Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N LYS H 102 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS H 206 " --> pdb=" O ARG H 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 236 " --> pdb=" O PHE H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 45' Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 110 Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N LYS I 102 " --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER I 163 " --> pdb=" O ILE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 236 " --> pdb=" O PHE I 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 110 Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N LYS J 102 " --> pdb=" O TYR J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL J 236 " --> pdb=" O PHE J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 45' Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 110 Proline residue: K 88 - end of helix removed outlier: 3.584A pdb=" N LYS K 102 " --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER K 163 " --> pdb=" O ILE K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 236 " --> pdb=" O PHE K 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 45' Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 110 Proline residue: L 88 - end of helix removed outlier: 3.584A pdb=" N LYS L 102 " --> pdb=" O TYR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.712A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5796 1.34 - 1.46: 4036 1.46 - 1.57: 10196 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 20148 Sorted by residual: bond pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.73e+00 bond pdb=" N HIS I 194 " pdb=" CA HIS I 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.67e+00 bond pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.65e+00 bond pdb=" N HIS J 194 " pdb=" CA HIS J 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.64e+00 bond pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.63e+00 ... (remaining 20143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 25803 1.54 - 3.08: 1229 3.08 - 4.62: 148 4.62 - 6.16: 60 6.16 - 7.70: 48 Bond angle restraints: 27288 Sorted by residual: angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO K 193 " pdb=" N HIS K 194 " pdb=" CA HIS K 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO H 193 " pdb=" N HIS H 194 " pdb=" CA HIS H 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.48e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 120.79 127.71 -6.92 1.39e+00 5.18e-01 2.48e+01 ... (remaining 27283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.95: 9458 11.95 - 23.89: 1534 23.89 - 35.84: 552 35.84 - 47.78: 192 47.78 - 59.73: 72 Dihedral angle restraints: 11808 sinusoidal: 4752 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.46 -26.46 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS I 61 " pdb=" SG CYS I 61 " pdb=" SG CYS I 192 " pdb=" CB CYS I 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.45 -26.45 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS F 61 " pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " pdb=" CB CYS F 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.44 -26.44 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 11805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3012 0.113 - 0.226: 60 0.226 - 0.340: 12 0.340 - 0.453: 0 0.453 - 0.566: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB ILE D 34 " pdb=" CA ILE D 34 " pdb=" CG1 ILE D 34 " pdb=" CG2 ILE D 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3093 not shown) Planarity restraints: 3300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 12 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CG ASP I 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP I 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 12 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" CG ASP K 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP K 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP K 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 12 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" CG ASP B 12 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP B 12 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 12 " -0.010 2.00e-02 2.50e+03 ... (remaining 3297 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4595 2.78 - 3.31: 16566 3.31 - 3.84: 31244 3.84 - 4.37: 31952 4.37 - 4.90: 59471 Nonbonded interactions: 143828 Sorted by model distance: nonbonded pdb=" O ILE K 72 " pdb=" OH TYR K 177 " model vdw 2.253 3.040 nonbonded pdb=" O ILE G 72 " pdb=" OH TYR G 177 " model vdw 2.253 3.040 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.253 3.040 nonbonded pdb=" O ILE D 72 " pdb=" OH TYR D 177 " model vdw 2.253 3.040 nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.253 3.040 ... (remaining 143823 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 0.034 20184 Z= 0.245 Angle : 0.827 7.699 27360 Z= 0.479 Chirality : 0.057 0.566 3096 Planarity : 0.006 0.040 3300 Dihedral : 14.697 59.726 7140 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.89 % Allowed : 2.27 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 2364 helix: -0.92 (0.10), residues: 1668 sheet: 1.27 (0.48), residues: 132 loop : -2.97 (0.20), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 101 TYR 0.011 0.001 TYR G 66 PHE 0.021 0.002 PHE H 212 TRP 0.011 0.001 TRP K 45 HIS 0.001 0.001 HIS I 194 Details of bonding type rmsd covalent geometry : bond 0.00512 (20148) covalent geometry : angle 0.82634 (27288) SS BOND : bond 0.00195 ( 36) SS BOND : angle 0.92773 ( 72) hydrogen bonds : bond 0.14580 ( 1368) hydrogen bonds : angle 4.67326 ( 4068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 524 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9041 (tttt) cc_final: 0.8539 (ttmm) REVERT: A 17 TYR cc_start: 0.8697 (m-80) cc_final: 0.8321 (m-10) REVERT: A 101 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7903 (mtp-110) REVERT: A 189 ARG cc_start: 0.8230 (ttt180) cc_final: 0.7900 (ttm170) REVERT: A 230 TYR cc_start: 0.7924 (t80) cc_final: 0.7563 (t80) REVERT: G 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8551 (ttmm) REVERT: G 17 TYR cc_start: 0.8780 (m-80) cc_final: 0.8483 (m-80) REVERT: G 47 ASP cc_start: 0.8968 (p0) cc_final: 0.8767 (p0) REVERT: G 109 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.6020 (tptt) REVERT: B 13 LYS cc_start: 0.8854 (tttt) cc_final: 0.8564 (ttmm) REVERT: B 47 ASP cc_start: 0.8936 (p0) cc_final: 0.8638 (p0) REVERT: B 101 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7736 (mtp-110) REVERT: B 230 TYR cc_start: 0.8049 (t80) cc_final: 0.7848 (t80) REVERT: C 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8486 (ttmm) REVERT: C 42 GLU cc_start: 0.8007 (tt0) cc_final: 0.7457 (tm-30) REVERT: C 47 ASP cc_start: 0.8860 (p0) cc_final: 0.8560 (p0) REVERT: C 53 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7495 (mtt180) REVERT: C 67 ASP cc_start: 0.8776 (t0) cc_final: 0.8541 (t0) REVERT: C 100 MET cc_start: 0.8482 (mtp) cc_final: 0.8123 (mtp) REVERT: C 189 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7446 (ttt180) REVERT: D 53 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7645 (mmt90) REVERT: D 62 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6964 (tt0) REVERT: D 227 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8269 (mm-30) REVERT: E 13 LYS cc_start: 0.8864 (tttt) cc_final: 0.8526 (ttmm) REVERT: E 42 GLU cc_start: 0.7911 (tt0) cc_final: 0.7510 (tm-30) REVERT: E 47 ASP cc_start: 0.8942 (p0) cc_final: 0.8641 (p0) REVERT: E 189 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8093 (ttm-80) REVERT: F 13 LYS cc_start: 0.8930 (tttt) cc_final: 0.8533 (ttmm) REVERT: F 17 TYR cc_start: 0.8737 (m-80) cc_final: 0.8421 (m-80) REVERT: F 53 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7579 (mtt180) REVERT: F 189 ARG cc_start: 0.8456 (ttt180) cc_final: 0.7975 (ttt180) REVERT: H 35 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (tt) REVERT: H 227 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8269 (mm-30) REVERT: H 230 TYR cc_start: 0.7833 (t80) cc_final: 0.7603 (t80) REVERT: I 13 LYS cc_start: 0.8793 (tttt) cc_final: 0.8377 (ttmm) REVERT: I 39 THR cc_start: 0.9215 (m) cc_final: 0.8808 (p) REVERT: I 53 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7665 (mtt180) REVERT: I 62 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7340 (mt-10) REVERT: J 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8498 (ttmm) REVERT: J 189 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8248 (ttm170) REVERT: K 13 LYS cc_start: 0.8935 (tttt) cc_final: 0.8535 (ttmm) REVERT: K 42 GLU cc_start: 0.7870 (tt0) cc_final: 0.7310 (tm-30) REVERT: K 47 ASP cc_start: 0.8978 (p0) cc_final: 0.8709 (p0) REVERT: K 185 TYR cc_start: 0.8408 (t80) cc_final: 0.8103 (t80) REVERT: K 189 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8281 (ttm170) REVERT: K 213 MET cc_start: 0.8981 (mmm) cc_final: 0.8776 (mmt) REVERT: L 13 LYS cc_start: 0.8861 (tttt) cc_final: 0.8463 (ttmm) REVERT: L 17 TYR cc_start: 0.8688 (m-80) cc_final: 0.8466 (m-80) REVERT: L 47 ASP cc_start: 0.8971 (p0) cc_final: 0.8718 (p0) REVERT: L 53 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7477 (mtt180) REVERT: L 189 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8033 (ttm-80) outliers start: 84 outliers final: 34 residues processed: 582 average time/residue: 0.1661 time to fit residues: 141.8661 Evaluate side-chains 469 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 433 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 87 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN B 194 HIS D 15 GLN H 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094595 restraints weight = 29133.713| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.53 r_work: 0.3017 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20184 Z= 0.161 Angle : 0.517 5.224 27360 Z= 0.280 Chirality : 0.035 0.129 3096 Planarity : 0.004 0.033 3300 Dihedral : 6.780 57.722 2654 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.38 % Allowed : 10.60 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2364 helix: 1.81 (0.12), residues: 1668 sheet: 2.08 (0.49), residues: 132 loop : -2.64 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.012 0.001 TYR E 230 PHE 0.013 0.001 PHE E 169 TRP 0.008 0.001 TRP C 45 HIS 0.002 0.001 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00373 (20148) covalent geometry : angle 0.51585 (27288) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.73961 ( 72) hydrogen bonds : bond 0.05564 ( 1368) hydrogen bonds : angle 3.14228 ( 4068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 450 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9020 (tttt) cc_final: 0.8560 (ttmm) REVERT: A 17 TYR cc_start: 0.8764 (m-80) cc_final: 0.8417 (m-10) REVERT: A 42 GLU cc_start: 0.8445 (tt0) cc_final: 0.7676 (tm-30) REVERT: A 67 ASP cc_start: 0.8672 (t0) cc_final: 0.8415 (t0) REVERT: A 230 TYR cc_start: 0.7782 (t80) cc_final: 0.7539 (t80) REVERT: G 13 LYS cc_start: 0.8926 (tttt) cc_final: 0.8565 (ttmm) REVERT: G 17 TYR cc_start: 0.8838 (m-80) cc_final: 0.8582 (m-80) REVERT: G 55 ASN cc_start: 0.9031 (t0) cc_final: 0.8668 (t0) REVERT: G 101 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7613 (mtp-110) REVERT: B 13 LYS cc_start: 0.8929 (tttt) cc_final: 0.8585 (ttmm) REVERT: B 47 ASP cc_start: 0.9136 (p0) cc_final: 0.8929 (p0) REVERT: B 101 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7789 (mtp-110) REVERT: C 13 LYS cc_start: 0.8943 (tttt) cc_final: 0.8539 (ttmm) REVERT: C 42 GLU cc_start: 0.8532 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 47 ASP cc_start: 0.9153 (p0) cc_final: 0.8936 (p0) REVERT: C 67 ASP cc_start: 0.8955 (t0) cc_final: 0.8729 (t0) REVERT: C 189 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7382 (ttt180) REVERT: D 13 LYS cc_start: 0.9040 (tttt) cc_final: 0.8682 (ttmm) REVERT: D 35 LEU cc_start: 0.9049 (tp) cc_final: 0.8666 (tt) REVERT: D 227 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8476 (mm-30) REVERT: E 13 LYS cc_start: 0.8869 (tttt) cc_final: 0.8640 (ttmm) REVERT: E 42 GLU cc_start: 0.8391 (tt0) cc_final: 0.7832 (tm-30) REVERT: E 47 ASP cc_start: 0.9141 (p0) cc_final: 0.8918 (p0) REVERT: E 189 ARG cc_start: 0.8237 (ttt180) cc_final: 0.7897 (ttm170) REVERT: F 13 LYS cc_start: 0.8905 (tttt) cc_final: 0.8570 (ttmm) REVERT: F 17 TYR cc_start: 0.8789 (m-80) cc_final: 0.8502 (m-80) REVERT: F 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8693 (t0) REVERT: H 13 LYS cc_start: 0.9036 (tttt) cc_final: 0.8664 (ttmm) REVERT: H 17 TYR cc_start: 0.8763 (m-80) cc_final: 0.8421 (m-10) REVERT: I 13 LYS cc_start: 0.8770 (tttt) cc_final: 0.8454 (ttmm) REVERT: J 13 LYS cc_start: 0.8909 (tttt) cc_final: 0.8604 (ttmm) REVERT: J 55 ASN cc_start: 0.9030 (t0) cc_final: 0.8627 (t0) REVERT: K 13 LYS cc_start: 0.9006 (tttt) cc_final: 0.8650 (ttmm) REVERT: K 42 GLU cc_start: 0.8447 (tt0) cc_final: 0.7731 (tm-30) REVERT: K 67 ASP cc_start: 0.8670 (t0) cc_final: 0.8255 (t0) REVERT: K 100 MET cc_start: 0.8656 (mtp) cc_final: 0.8397 (mtm) REVERT: K 212 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8045 (t80) REVERT: L 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8628 (ttmm) REVERT: L 17 TYR cc_start: 0.8684 (m-80) cc_final: 0.8439 (m-80) REVERT: L 47 ASP cc_start: 0.9181 (p0) cc_final: 0.8958 (p0) REVERT: L 101 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7814 (mtp-110) outliers start: 73 outliers final: 31 residues processed: 483 average time/residue: 0.1623 time to fit residues: 116.2701 Evaluate side-chains 469 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 437 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094919 restraints weight = 29251.271| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.56 r_work: 0.3030 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20184 Z= 0.145 Angle : 0.477 5.236 27360 Z= 0.258 Chirality : 0.035 0.124 3096 Planarity : 0.003 0.029 3300 Dihedral : 4.286 57.619 2600 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.59 % Allowed : 13.15 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.17), residues: 2364 helix: 2.56 (0.12), residues: 1668 sheet: 2.31 (0.48), residues: 132 loop : -2.38 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 101 TYR 0.018 0.001 TYR H 230 PHE 0.014 0.001 PHE G 169 TRP 0.007 0.001 TRP C 45 HIS 0.002 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00332 (20148) covalent geometry : angle 0.47618 (27288) SS BOND : bond 0.00162 ( 36) SS BOND : angle 0.71866 ( 72) hydrogen bonds : bond 0.05014 ( 1368) hydrogen bonds : angle 2.94871 ( 4068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 446 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9038 (tttt) cc_final: 0.8602 (ttmm) REVERT: A 17 TYR cc_start: 0.8781 (m-80) cc_final: 0.8451 (m-10) REVERT: A 42 GLU cc_start: 0.8438 (tt0) cc_final: 0.7660 (tm-30) REVERT: A 67 ASP cc_start: 0.8716 (t0) cc_final: 0.8405 (t0) REVERT: A 230 TYR cc_start: 0.7848 (t80) cc_final: 0.7571 (t80) REVERT: G 13 LYS cc_start: 0.8921 (tttt) cc_final: 0.8559 (ttmm) REVERT: G 17 TYR cc_start: 0.8848 (m-80) cc_final: 0.8578 (m-80) REVERT: G 42 GLU cc_start: 0.8462 (tt0) cc_final: 0.7654 (tm-30) REVERT: G 55 ASN cc_start: 0.9060 (t0) cc_final: 0.8723 (t0) REVERT: B 13 LYS cc_start: 0.8916 (tttt) cc_final: 0.8575 (ttmm) REVERT: B 47 ASP cc_start: 0.9116 (p0) cc_final: 0.8900 (p0) REVERT: B 189 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7769 (ttm170) REVERT: C 13 LYS cc_start: 0.8924 (tttt) cc_final: 0.8570 (ttmm) REVERT: C 35 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8533 (tp) REVERT: C 42 GLU cc_start: 0.8494 (tt0) cc_final: 0.7904 (tm-30) REVERT: C 47 ASP cc_start: 0.9118 (p0) cc_final: 0.8882 (p0) REVERT: C 189 ARG cc_start: 0.7869 (ttt180) cc_final: 0.7612 (ttt180) REVERT: D 13 LYS cc_start: 0.8989 (tttt) cc_final: 0.8617 (ttmm) REVERT: D 35 LEU cc_start: 0.8967 (tp) cc_final: 0.8637 (tt) REVERT: D 42 GLU cc_start: 0.8313 (tt0) cc_final: 0.7695 (tm-30) REVERT: D 67 ASP cc_start: 0.8668 (t0) cc_final: 0.8334 (t0) REVERT: D 106 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6046 (mp) REVERT: D 227 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8403 (mm-30) REVERT: E 13 LYS cc_start: 0.8927 (tttt) cc_final: 0.8541 (ttmm) REVERT: E 42 GLU cc_start: 0.8397 (tt0) cc_final: 0.7860 (tm-30) REVERT: E 47 ASP cc_start: 0.9093 (p0) cc_final: 0.8881 (p0) REVERT: F 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8554 (ttmm) REVERT: F 17 TYR cc_start: 0.8814 (m-80) cc_final: 0.8480 (m-80) REVERT: F 42 GLU cc_start: 0.8472 (tt0) cc_final: 0.7769 (tm-30) REVERT: F 55 ASN cc_start: 0.9059 (t0) cc_final: 0.8705 (t0) REVERT: H 11 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8399 (mp) REVERT: H 13 LYS cc_start: 0.9003 (tttt) cc_final: 0.8604 (ttmm) REVERT: H 17 TYR cc_start: 0.8794 (m-80) cc_final: 0.8585 (m-80) REVERT: H 42 GLU cc_start: 0.8351 (tt0) cc_final: 0.7716 (tm-30) REVERT: I 13 LYS cc_start: 0.8888 (tttt) cc_final: 0.8528 (ttmm) REVERT: I 17 TYR cc_start: 0.8735 (m-80) cc_final: 0.8498 (m-80) REVERT: J 13 LYS cc_start: 0.8882 (tttt) cc_final: 0.8581 (ttmm) REVERT: J 42 GLU cc_start: 0.8465 (tt0) cc_final: 0.7780 (tm-30) REVERT: J 55 ASN cc_start: 0.9045 (t0) cc_final: 0.8657 (t0) REVERT: K 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8666 (ttmm) REVERT: K 42 GLU cc_start: 0.8414 (tt0) cc_final: 0.7685 (tm-30) REVERT: K 67 ASP cc_start: 0.8625 (t0) cc_final: 0.8366 (t0) REVERT: K 100 MET cc_start: 0.8553 (mtp) cc_final: 0.8313 (mtm) REVERT: K 212 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8055 (t80) REVERT: L 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8551 (ttmm) REVERT: L 17 TYR cc_start: 0.8687 (m-80) cc_final: 0.8472 (m-80) REVERT: L 42 GLU cc_start: 0.8428 (tt0) cc_final: 0.7724 (tm-30) REVERT: L 47 ASP cc_start: 0.9148 (p0) cc_final: 0.8928 (p0) REVERT: L 67 ASP cc_start: 0.8874 (t0) cc_final: 0.8648 (t0) REVERT: L 101 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7791 (mtp-110) outliers start: 56 outliers final: 34 residues processed: 474 average time/residue: 0.1601 time to fit residues: 113.0834 Evaluate side-chains 473 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 435 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 191 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 84 optimal weight: 0.0370 overall best weight: 1.6462 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.126680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095741 restraints weight = 29190.968| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.55 r_work: 0.3049 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20184 Z= 0.135 Angle : 0.461 5.279 27360 Z= 0.248 Chirality : 0.034 0.137 3096 Planarity : 0.003 0.030 3300 Dihedral : 3.409 13.259 2592 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.73 % Allowed : 14.44 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.17), residues: 2364 helix: 2.85 (0.12), residues: 1668 sheet: 2.44 (0.47), residues: 132 loop : -2.19 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 101 TYR 0.010 0.001 TYR A 175 PHE 0.012 0.001 PHE A 32 TRP 0.005 0.001 TRP G 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00310 (20148) covalent geometry : angle 0.46014 (27288) SS BOND : bond 0.00123 ( 36) SS BOND : angle 0.67136 ( 72) hydrogen bonds : bond 0.04694 ( 1368) hydrogen bonds : angle 2.81957 ( 4068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 455 time to evaluate : 0.474 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 13 LYS cc_start: 0.9046 (tttt) cc_final: 0.8606 (ttmm) REVERT: A 17 TYR cc_start: 0.8762 (m-80) cc_final: 0.8513 (m-10) REVERT: A 42 GLU cc_start: 0.8431 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 67 ASP cc_start: 0.8710 (t0) cc_final: 0.8365 (t0) REVERT: A 230 TYR cc_start: 0.7902 (t80) cc_final: 0.7632 (t80) REVERT: G 13 LYS cc_start: 0.8961 (tttt) cc_final: 0.8629 (ttmm) REVERT: G 42 GLU cc_start: 0.8431 (tt0) cc_final: 0.7664 (tm-30) REVERT: G 55 ASN cc_start: 0.9037 (t0) cc_final: 0.8702 (t0) REVERT: B 13 LYS cc_start: 0.8906 (tttt) cc_final: 0.8588 (ttmm) REVERT: B 42 GLU cc_start: 0.8369 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 47 ASP cc_start: 0.9097 (p0) cc_final: 0.8867 (p0) REVERT: B 67 ASP cc_start: 0.8772 (t0) cc_final: 0.8531 (t0) REVERT: C 13 LYS cc_start: 0.8965 (tttt) cc_final: 0.8630 (ttmm) REVERT: C 35 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8535 (tp) REVERT: C 42 GLU cc_start: 0.8515 (tt0) cc_final: 0.7899 (tm-30) REVERT: C 47 ASP cc_start: 0.9101 (p0) cc_final: 0.8855 (p0) REVERT: D 13 LYS cc_start: 0.8988 (tttt) cc_final: 0.8618 (ttmm) REVERT: D 35 LEU cc_start: 0.8933 (tp) cc_final: 0.8713 (tt) REVERT: D 42 GLU cc_start: 0.8412 (tt0) cc_final: 0.7751 (tm-30) REVERT: D 67 ASP cc_start: 0.8686 (t0) cc_final: 0.8331 (t0) REVERT: D 106 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5821 (mp) REVERT: E 13 LYS cc_start: 0.8913 (tttt) cc_final: 0.8492 (ttmm) REVERT: E 42 GLU cc_start: 0.8382 (tt0) cc_final: 0.7858 (tm-30) REVERT: E 47 ASP cc_start: 0.9106 (p0) cc_final: 0.8849 (p0) REVERT: E 67 ASP cc_start: 0.8827 (t0) cc_final: 0.8578 (t0) REVERT: E 101 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7734 (mtp-110) REVERT: F 13 LYS cc_start: 0.8914 (tttt) cc_final: 0.8582 (ttmm) REVERT: F 42 GLU cc_start: 0.8542 (tt0) cc_final: 0.7819 (tm-30) REVERT: F 55 ASN cc_start: 0.9052 (t0) cc_final: 0.8699 (t0) REVERT: H 11 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (mp) REVERT: H 13 LYS cc_start: 0.8991 (tttt) cc_final: 0.8623 (ttmm) REVERT: H 42 GLU cc_start: 0.8328 (tt0) cc_final: 0.7692 (tm-30) REVERT: I 13 LYS cc_start: 0.8912 (tttt) cc_final: 0.8487 (ttmm) REVERT: J 13 LYS cc_start: 0.8897 (tttt) cc_final: 0.8592 (ttmm) REVERT: J 42 GLU cc_start: 0.8538 (tt0) cc_final: 0.7826 (tm-30) REVERT: J 55 ASN cc_start: 0.9044 (t0) cc_final: 0.8668 (t0) REVERT: K 13 LYS cc_start: 0.9009 (tttt) cc_final: 0.8683 (ttmm) REVERT: K 42 GLU cc_start: 0.8496 (tt0) cc_final: 0.7706 (tm-30) REVERT: K 55 ASN cc_start: 0.9059 (t0) cc_final: 0.8851 (t0) REVERT: K 100 MET cc_start: 0.8547 (mtp) cc_final: 0.8305 (mtm) REVERT: K 212 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8126 (t80) REVERT: L 13 LYS cc_start: 0.8941 (tttt) cc_final: 0.8554 (ttmm) REVERT: L 42 GLU cc_start: 0.8353 (tt0) cc_final: 0.7705 (tm-30) REVERT: L 47 ASP cc_start: 0.9138 (p0) cc_final: 0.8925 (p0) REVERT: L 67 ASP cc_start: 0.8914 (t0) cc_final: 0.8653 (t0) REVERT: L 101 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7775 (mtp-110) outliers start: 59 outliers final: 38 residues processed: 483 average time/residue: 0.1487 time to fit residues: 107.0764 Evaluate side-chains 486 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 444 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 204 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098914 restraints weight = 29080.367| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.55 r_work: 0.3097 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20184 Z= 0.106 Angle : 0.430 5.413 27360 Z= 0.233 Chirality : 0.034 0.150 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.215 13.033 2592 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.62 % Allowed : 16.85 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.17), residues: 2364 helix: 3.04 (0.12), residues: 1668 sheet: 2.37 (0.47), residues: 132 loop : -2.11 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.009 0.001 TYR L 17 PHE 0.011 0.001 PHE J 169 TRP 0.005 0.001 TRP K 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00224 (20148) covalent geometry : angle 0.42941 (27288) SS BOND : bond 0.00087 ( 36) SS BOND : angle 0.56128 ( 72) hydrogen bonds : bond 0.04026 ( 1368) hydrogen bonds : angle 2.68066 ( 4068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 486 time to evaluate : 0.818 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 42 GLU cc_start: 0.8351 (tt0) cc_final: 0.7639 (tm-30) REVERT: A 67 ASP cc_start: 0.8670 (t0) cc_final: 0.8321 (t0) REVERT: A 230 TYR cc_start: 0.7843 (t80) cc_final: 0.7575 (t80) REVERT: G 13 LYS cc_start: 0.8936 (tttt) cc_final: 0.8595 (ttmm) REVERT: G 42 GLU cc_start: 0.8442 (tt0) cc_final: 0.7733 (tm-30) REVERT: G 55 ASN cc_start: 0.8972 (t0) cc_final: 0.8636 (t0) REVERT: B 13 LYS cc_start: 0.8916 (tttt) cc_final: 0.8591 (ttmm) REVERT: B 42 GLU cc_start: 0.8301 (tt0) cc_final: 0.7673 (tm-30) REVERT: B 47 ASP cc_start: 0.9087 (p0) cc_final: 0.8842 (p0) REVERT: B 67 ASP cc_start: 0.8744 (t0) cc_final: 0.8422 (t0) REVERT: C 13 LYS cc_start: 0.8955 (tttt) cc_final: 0.8613 (ttmm) REVERT: C 35 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8517 (tp) REVERT: C 42 GLU cc_start: 0.8514 (tt0) cc_final: 0.7915 (tm-30) REVERT: C 47 ASP cc_start: 0.9115 (p0) cc_final: 0.8876 (p0) REVERT: C 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8707 (t0) REVERT: D 13 LYS cc_start: 0.8975 (tttt) cc_final: 0.8609 (ttmm) REVERT: D 42 GLU cc_start: 0.8457 (tt0) cc_final: 0.7763 (tm-30) REVERT: D 67 ASP cc_start: 0.8670 (t0) cc_final: 0.8310 (t0) REVERT: D 106 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5786 (mp) REVERT: E 13 LYS cc_start: 0.8912 (tttt) cc_final: 0.8469 (ttmm) REVERT: E 42 GLU cc_start: 0.8275 (tt0) cc_final: 0.7813 (tm-30) REVERT: E 47 ASP cc_start: 0.9079 (p0) cc_final: 0.8825 (p0) REVERT: E 101 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7782 (mtp-110) REVERT: F 13 LYS cc_start: 0.8902 (tttt) cc_final: 0.8591 (ttmm) REVERT: F 42 GLU cc_start: 0.8428 (tt0) cc_final: 0.7734 (tm-30) REVERT: F 55 ASN cc_start: 0.8959 (t0) cc_final: 0.8640 (t0) REVERT: H 11 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8388 (mp) REVERT: H 13 LYS cc_start: 0.8992 (tttt) cc_final: 0.8625 (ttmm) REVERT: H 42 GLU cc_start: 0.8448 (tt0) cc_final: 0.7727 (tm-30) REVERT: H 106 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5776 (mp) REVERT: I 13 LYS cc_start: 0.8874 (tttt) cc_final: 0.8553 (ttmm) REVERT: I 42 GLU cc_start: 0.8416 (tt0) cc_final: 0.7747 (tm-30) REVERT: I 101 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7638 (mtp-110) REVERT: J 13 LYS cc_start: 0.8891 (tttt) cc_final: 0.8590 (ttmm) REVERT: J 42 GLU cc_start: 0.8443 (tt0) cc_final: 0.7762 (tm-30) REVERT: J 55 ASN cc_start: 0.8964 (t0) cc_final: 0.8646 (t0) REVERT: K 13 LYS cc_start: 0.9006 (tttt) cc_final: 0.8697 (ttmm) REVERT: K 42 GLU cc_start: 0.8389 (tt0) cc_final: 0.7564 (tm-30) REVERT: K 67 ASP cc_start: 0.8791 (t0) cc_final: 0.8555 (t0) REVERT: K 212 PHE cc_start: 0.8309 (m-80) cc_final: 0.8031 (t80) REVERT: L 13 LYS cc_start: 0.8894 (tttt) cc_final: 0.8531 (ttmm) REVERT: L 42 GLU cc_start: 0.8314 (tt0) cc_final: 0.7809 (tm-30) REVERT: L 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8883 (p0) REVERT: L 67 ASP cc_start: 0.8895 (t0) cc_final: 0.8594 (t0) REVERT: L 101 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7710 (mtp-110) REVERT: L 189 ARG cc_start: 0.8131 (ttt180) cc_final: 0.7847 (ttt180) outliers start: 35 outliers final: 26 residues processed: 499 average time/residue: 0.1563 time to fit residues: 116.1672 Evaluate side-chains 489 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 459 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 chunk 202 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 221 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.128257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097787 restraints weight = 28956.775| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.54 r_work: 0.3021 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20184 Z= 0.126 Angle : 0.452 5.919 27360 Z= 0.243 Chirality : 0.034 0.154 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.190 12.240 2592 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.81 % Allowed : 16.90 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.17), residues: 2364 helix: 3.13 (0.12), residues: 1668 sheet: 2.38 (0.47), residues: 132 loop : -2.04 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 101 TYR 0.017 0.001 TYR J 66 PHE 0.016 0.001 PHE B 169 TRP 0.003 0.001 TRP F 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00290 (20148) covalent geometry : angle 0.45100 (27288) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.61671 ( 72) hydrogen bonds : bond 0.04240 ( 1368) hydrogen bonds : angle 2.69294 ( 4068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 464 time to evaluate : 0.835 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 42 GLU cc_start: 0.8357 (tt0) cc_final: 0.7551 (tm-30) REVERT: A 67 ASP cc_start: 0.8722 (t0) cc_final: 0.8348 (t0) REVERT: A 230 TYR cc_start: 0.7856 (t80) cc_final: 0.7603 (t80) REVERT: G 13 LYS cc_start: 0.8971 (tttt) cc_final: 0.8661 (ttmm) REVERT: G 42 GLU cc_start: 0.8492 (tt0) cc_final: 0.7800 (tm-30) REVERT: G 55 ASN cc_start: 0.9015 (t0) cc_final: 0.8660 (t0) REVERT: B 13 LYS cc_start: 0.8893 (tttt) cc_final: 0.8552 (ttmm) REVERT: B 42 GLU cc_start: 0.8339 (tt0) cc_final: 0.7716 (tm-30) REVERT: B 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8867 (p0) REVERT: B 67 ASP cc_start: 0.8804 (t0) cc_final: 0.8520 (t0) REVERT: B 101 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7736 (mtp-110) REVERT: C 13 LYS cc_start: 0.8947 (tttt) cc_final: 0.8624 (ttmm) REVERT: C 35 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8624 (tp) REVERT: C 42 GLU cc_start: 0.8570 (tt0) cc_final: 0.7968 (tm-30) REVERT: C 47 ASP cc_start: 0.9132 (p0) cc_final: 0.8879 (p0) REVERT: C 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8732 (t0) REVERT: D 13 LYS cc_start: 0.8973 (tttt) cc_final: 0.8609 (ttmm) REVERT: D 35 LEU cc_start: 0.8928 (tp) cc_final: 0.8698 (tt) REVERT: D 42 GLU cc_start: 0.8527 (tt0) cc_final: 0.7668 (tm-30) REVERT: D 67 ASP cc_start: 0.8717 (t0) cc_final: 0.8375 (t0) REVERT: D 106 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5720 (mp) REVERT: E 13 LYS cc_start: 0.8830 (tttt) cc_final: 0.8467 (ttmm) REVERT: E 42 GLU cc_start: 0.8324 (tt0) cc_final: 0.7869 (tm-30) REVERT: E 47 ASP cc_start: 0.9107 (p0) cc_final: 0.8867 (p0) REVERT: E 101 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7733 (mtp-110) REVERT: F 13 LYS cc_start: 0.8910 (tttt) cc_final: 0.8611 (ttmm) REVERT: F 42 GLU cc_start: 0.8461 (tt0) cc_final: 0.7776 (tm-30) REVERT: F 55 ASN cc_start: 0.9024 (t0) cc_final: 0.8680 (t0) REVERT: H 11 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8389 (mp) REVERT: H 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8605 (ttmm) REVERT: H 42 GLU cc_start: 0.8393 (tt0) cc_final: 0.7568 (tm-30) REVERT: H 106 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5779 (mp) REVERT: I 13 LYS cc_start: 0.8868 (tttt) cc_final: 0.8525 (ttmm) REVERT: I 42 GLU cc_start: 0.8401 (tt0) cc_final: 0.7717 (tm-30) REVERT: I 101 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7633 (mtp-110) REVERT: J 13 LYS cc_start: 0.8881 (tttt) cc_final: 0.8576 (ttmm) REVERT: J 42 GLU cc_start: 0.8444 (tt0) cc_final: 0.7765 (tm-30) REVERT: J 55 ASN cc_start: 0.9017 (t0) cc_final: 0.8657 (t0) REVERT: K 13 LYS cc_start: 0.9021 (tttt) cc_final: 0.8658 (ttmm) REVERT: K 42 GLU cc_start: 0.8448 (tt0) cc_final: 0.7638 (tm-30) REVERT: K 55 ASN cc_start: 0.9022 (t0) cc_final: 0.8821 (t0) REVERT: K 67 ASP cc_start: 0.8778 (t0) cc_final: 0.8523 (t0) REVERT: K 212 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8125 (t80) REVERT: L 13 LYS cc_start: 0.8878 (tttt) cc_final: 0.8530 (ttmm) REVERT: L 42 GLU cc_start: 0.8351 (tt0) cc_final: 0.7856 (tm-30) REVERT: L 47 ASP cc_start: 0.9122 (p0) cc_final: 0.8886 (p0) REVERT: L 67 ASP cc_start: 0.8937 (t0) cc_final: 0.8713 (t0) REVERT: L 101 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7711 (mtp-110) outliers start: 39 outliers final: 26 residues processed: 480 average time/residue: 0.1676 time to fit residues: 118.6251 Evaluate side-chains 490 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 459 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 144 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 228 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099506 restraints weight = 28941.969| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.56 r_work: 0.3087 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20184 Z= 0.103 Angle : 0.431 5.427 27360 Z= 0.233 Chirality : 0.033 0.156 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.089 12.126 2592 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.34 % Allowed : 17.55 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.17), residues: 2364 helix: 3.25 (0.12), residues: 1668 sheet: 2.29 (0.47), residues: 132 loop : -2.00 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 101 TYR 0.021 0.001 TYR J 230 PHE 0.011 0.001 PHE A 32 TRP 0.005 0.001 TRP F 45 HIS 0.001 0.000 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00220 (20148) covalent geometry : angle 0.43108 (27288) SS BOND : bond 0.00082 ( 36) SS BOND : angle 0.55545 ( 72) hydrogen bonds : bond 0.03786 ( 1368) hydrogen bonds : angle 2.61953 ( 4068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 487 time to evaluate : 0.776 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 13 LYS cc_start: 0.9050 (tttt) cc_final: 0.8643 (ttmm) REVERT: A 42 GLU cc_start: 0.8302 (tt0) cc_final: 0.7422 (tm-30) REVERT: A 67 ASP cc_start: 0.8692 (t0) cc_final: 0.8319 (t0) REVERT: G 13 LYS cc_start: 0.8965 (tttt) cc_final: 0.8672 (ttmm) REVERT: G 15 GLN cc_start: 0.8877 (mt0) cc_final: 0.8618 (mt0) REVERT: G 42 GLU cc_start: 0.8471 (tt0) cc_final: 0.7761 (tm-30) REVERT: G 55 ASN cc_start: 0.8940 (t0) cc_final: 0.8625 (t0) REVERT: G 224 ASN cc_start: 0.8825 (m-40) cc_final: 0.8623 (m-40) REVERT: B 13 LYS cc_start: 0.8890 (tttt) cc_final: 0.8536 (ttmm) REVERT: B 42 GLU cc_start: 0.8307 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 47 ASP cc_start: 0.9089 (p0) cc_final: 0.8846 (p0) REVERT: B 67 ASP cc_start: 0.8739 (t0) cc_final: 0.8395 (t0) REVERT: B 101 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7745 (mtp-110) REVERT: B 230 TYR cc_start: 0.7690 (t80) cc_final: 0.7345 (t80) REVERT: C 13 LYS cc_start: 0.8944 (tttt) cc_final: 0.8617 (ttmm) REVERT: C 35 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8599 (tp) REVERT: C 42 GLU cc_start: 0.8492 (tt0) cc_final: 0.7873 (tm-30) REVERT: C 47 ASP cc_start: 0.9133 (p0) cc_final: 0.8878 (p0) REVERT: C 55 ASN cc_start: 0.8966 (t0) cc_final: 0.8680 (t0) REVERT: D 13 LYS cc_start: 0.8966 (tttt) cc_final: 0.8613 (ttmm) REVERT: D 42 GLU cc_start: 0.8325 (tt0) cc_final: 0.7520 (tm-30) REVERT: D 67 ASP cc_start: 0.8691 (t0) cc_final: 0.8331 (t0) REVERT: D 106 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5790 (mp) REVERT: E 13 LYS cc_start: 0.8902 (tttt) cc_final: 0.8504 (ttmm) REVERT: E 39 THR cc_start: 0.8875 (m) cc_final: 0.8632 (m) REVERT: E 42 GLU cc_start: 0.8362 (tt0) cc_final: 0.7831 (tm-30) REVERT: E 47 ASP cc_start: 0.9075 (p0) cc_final: 0.8834 (p0) REVERT: E 101 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7686 (mtp-110) REVERT: E 189 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7798 (ttt180) REVERT: F 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8592 (ttmm) REVERT: F 42 GLU cc_start: 0.8426 (tt0) cc_final: 0.7754 (tm-30) REVERT: F 55 ASN cc_start: 0.8917 (t0) cc_final: 0.8587 (t0) REVERT: H 11 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8319 (mp) REVERT: H 13 LYS cc_start: 0.8967 (tttt) cc_final: 0.8598 (ttmm) REVERT: H 42 GLU cc_start: 0.8395 (tt0) cc_final: 0.7512 (tm-30) REVERT: H 106 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5742 (mp) REVERT: I 13 LYS cc_start: 0.8854 (tttt) cc_final: 0.8492 (ttmm) REVERT: I 42 GLU cc_start: 0.8328 (tt0) cc_final: 0.7667 (tm-30) REVERT: I 101 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7569 (mtp-110) REVERT: J 13 LYS cc_start: 0.8890 (tttt) cc_final: 0.8601 (ttmm) REVERT: J 42 GLU cc_start: 0.8414 (tt0) cc_final: 0.7759 (tm-30) REVERT: J 55 ASN cc_start: 0.8916 (t0) cc_final: 0.8584 (t0) REVERT: K 13 LYS cc_start: 0.9002 (tttt) cc_final: 0.8676 (ttmm) REVERT: K 42 GLU cc_start: 0.8421 (tt0) cc_final: 0.7615 (tm-30) REVERT: K 55 ASN cc_start: 0.8987 (t0) cc_final: 0.8777 (t0) REVERT: K 67 ASP cc_start: 0.8781 (t0) cc_final: 0.8522 (t0) REVERT: K 212 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7995 (t80) REVERT: L 13 LYS cc_start: 0.8868 (tttt) cc_final: 0.8512 (ttmm) REVERT: L 42 GLU cc_start: 0.8372 (tt0) cc_final: 0.7832 (tm-30) REVERT: L 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8861 (p0) REVERT: L 67 ASP cc_start: 0.8913 (t0) cc_final: 0.8625 (t0) REVERT: L 101 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7709 (mtp-110) REVERT: L 189 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7812 (ttt180) outliers start: 29 outliers final: 20 residues processed: 495 average time/residue: 0.1632 time to fit residues: 119.5115 Evaluate side-chains 501 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 476 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.127563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096640 restraints weight = 28954.795| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.54 r_work: 0.3053 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20184 Z= 0.128 Angle : 0.460 6.499 27360 Z= 0.247 Chirality : 0.034 0.153 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.092 11.721 2592 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.62 % Allowed : 17.69 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.17), residues: 2364 helix: 3.25 (0.12), residues: 1680 sheet: 2.33 (0.47), residues: 132 loop : -1.88 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 101 TYR 0.019 0.001 TYR A 230 PHE 0.011 0.001 PHE A 32 TRP 0.004 0.001 TRP G 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00295 (20148) covalent geometry : angle 0.46006 (27288) SS BOND : bond 0.00099 ( 36) SS BOND : angle 0.58848 ( 72) hydrogen bonds : bond 0.04212 ( 1368) hydrogen bonds : angle 2.66336 ( 4068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 465 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9056 (tttt) cc_final: 0.8650 (ttmm) REVERT: A 42 GLU cc_start: 0.8330 (tt0) cc_final: 0.7440 (tm-30) REVERT: A 67 ASP cc_start: 0.8730 (t0) cc_final: 0.8379 (t0) REVERT: G 13 LYS cc_start: 0.8973 (tttt) cc_final: 0.8645 (ttmm) REVERT: G 15 GLN cc_start: 0.8941 (mt0) cc_final: 0.8710 (mt0) REVERT: G 42 GLU cc_start: 0.8418 (tt0) cc_final: 0.7726 (tm-30) REVERT: G 55 ASN cc_start: 0.9016 (t0) cc_final: 0.8659 (t0) REVERT: B 13 LYS cc_start: 0.8881 (tttt) cc_final: 0.8547 (ttmm) REVERT: B 42 GLU cc_start: 0.8309 (tt0) cc_final: 0.7685 (tm-30) REVERT: B 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8869 (p0) REVERT: B 67 ASP cc_start: 0.8829 (t0) cc_final: 0.8507 (t0) REVERT: B 101 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7740 (mtp-110) REVERT: C 13 LYS cc_start: 0.8915 (tttt) cc_final: 0.8590 (ttmm) REVERT: C 42 GLU cc_start: 0.8506 (tt0) cc_final: 0.7864 (tm-30) REVERT: C 47 ASP cc_start: 0.9094 (p0) cc_final: 0.8835 (p0) REVERT: C 55 ASN cc_start: 0.9034 (t0) cc_final: 0.8694 (t0) REVERT: D 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8632 (ttmm) REVERT: D 42 GLU cc_start: 0.8361 (tt0) cc_final: 0.7531 (tm-30) REVERT: D 67 ASP cc_start: 0.8755 (t0) cc_final: 0.8409 (t0) REVERT: D 106 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5717 (mp) REVERT: E 13 LYS cc_start: 0.8855 (tttt) cc_final: 0.8466 (ttmm) REVERT: E 39 THR cc_start: 0.8887 (m) cc_final: 0.8651 (m) REVERT: E 42 GLU cc_start: 0.8357 (tt0) cc_final: 0.7834 (tm-30) REVERT: E 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8851 (p0) REVERT: E 101 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7644 (mtp-110) REVERT: F 13 LYS cc_start: 0.8949 (tttt) cc_final: 0.8653 (ttmm) REVERT: F 42 GLU cc_start: 0.8426 (tt0) cc_final: 0.7759 (tm-30) REVERT: F 55 ASN cc_start: 0.9030 (t0) cc_final: 0.8680 (t0) REVERT: H 11 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8293 (mp) REVERT: H 13 LYS cc_start: 0.9017 (tttt) cc_final: 0.8650 (ttmm) REVERT: H 42 GLU cc_start: 0.8415 (tt0) cc_final: 0.7540 (tm-30) REVERT: H 106 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5630 (mp) REVERT: H 227 GLU cc_start: 0.8778 (tp30) cc_final: 0.8478 (mm-30) REVERT: I 13 LYS cc_start: 0.8846 (tttt) cc_final: 0.8485 (ttmm) REVERT: I 42 GLU cc_start: 0.8338 (tt0) cc_final: 0.7677 (tm-30) REVERT: I 101 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7610 (mtp-110) REVERT: J 13 LYS cc_start: 0.8936 (tttt) cc_final: 0.8647 (ttmm) REVERT: J 42 GLU cc_start: 0.8433 (tt0) cc_final: 0.7774 (tm-30) REVERT: J 55 ASN cc_start: 0.9031 (t0) cc_final: 0.8665 (t0) REVERT: J 231 VAL cc_start: 0.8344 (t) cc_final: 0.8142 (p) REVERT: K 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8617 (ttmm) REVERT: K 42 GLU cc_start: 0.8360 (tt0) cc_final: 0.7519 (tm-30) REVERT: K 55 ASN cc_start: 0.9043 (t0) cc_final: 0.8833 (t0) REVERT: K 67 ASP cc_start: 0.8814 (t0) cc_final: 0.8565 (t0) REVERT: K 212 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8078 (t80) REVERT: L 13 LYS cc_start: 0.8850 (tttt) cc_final: 0.8486 (ttmm) REVERT: L 35 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8297 (tp) REVERT: L 39 THR cc_start: 0.8912 (m) cc_final: 0.8662 (m) REVERT: L 42 GLU cc_start: 0.8313 (tt0) cc_final: 0.7842 (tm-30) REVERT: L 47 ASP cc_start: 0.9116 (p0) cc_final: 0.8879 (p0) REVERT: L 67 ASP cc_start: 0.8930 (t0) cc_final: 0.8695 (t0) REVERT: L 101 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7712 (mtp-110) REVERT: L 189 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7836 (ttm170) outliers start: 35 outliers final: 27 residues processed: 478 average time/residue: 0.1727 time to fit residues: 121.8839 Evaluate side-chains 494 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 462 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 102 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 237 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 184 optimal weight: 0.0020 chunk 130 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 185 optimal weight: 0.0670 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN D 55 ASN F 15 GLN I 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100695 restraints weight = 28590.858| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.55 r_work: 0.3123 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20184 Z= 0.099 Angle : 0.433 5.436 27360 Z= 0.233 Chirality : 0.033 0.178 3096 Planarity : 0.003 0.029 3300 Dihedral : 2.998 12.491 2592 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.30 % Allowed : 18.19 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.17), residues: 2364 helix: 3.44 (0.12), residues: 1668 sheet: 2.27 (0.46), residues: 132 loop : -1.91 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 101 TYR 0.023 0.001 TYR J 230 PHE 0.010 0.001 PHE A 32 TRP 0.005 0.001 TRP G 45 HIS 0.001 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00204 (20148) covalent geometry : angle 0.43272 (27288) SS BOND : bond 0.00101 ( 36) SS BOND : angle 0.54567 ( 72) hydrogen bonds : bond 0.03403 ( 1368) hydrogen bonds : angle 2.56819 ( 4068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 509 time to evaluate : 0.819 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 13 LYS cc_start: 0.9053 (tttt) cc_final: 0.8669 (ttmm) REVERT: A 42 GLU cc_start: 0.8326 (tt0) cc_final: 0.7457 (tm-30) REVERT: A 67 ASP cc_start: 0.8662 (t0) cc_final: 0.8277 (t0) REVERT: G 13 LYS cc_start: 0.8934 (tttt) cc_final: 0.8619 (ttmm) REVERT: G 15 GLN cc_start: 0.8942 (mt0) cc_final: 0.8689 (mt0) REVERT: G 42 GLU cc_start: 0.8528 (tt0) cc_final: 0.7766 (tm-30) REVERT: G 55 ASN cc_start: 0.8868 (t0) cc_final: 0.8543 (t0) REVERT: G 224 ASN cc_start: 0.8787 (m-40) cc_final: 0.8570 (m-40) REVERT: B 13 LYS cc_start: 0.8885 (tttt) cc_final: 0.8554 (ttmm) REVERT: B 39 THR cc_start: 0.8806 (m) cc_final: 0.8571 (m) REVERT: B 42 GLU cc_start: 0.8336 (tt0) cc_final: 0.7711 (tm-30) REVERT: B 47 ASP cc_start: 0.9085 (p0) cc_final: 0.8840 (p0) REVERT: B 101 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7736 (mtp-110) REVERT: C 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8585 (ttmm) REVERT: C 42 GLU cc_start: 0.8510 (tt0) cc_final: 0.7880 (tm-30) REVERT: C 47 ASP cc_start: 0.9072 (p0) cc_final: 0.8804 (p0) REVERT: C 55 ASN cc_start: 0.8900 (t0) cc_final: 0.8594 (t0) REVERT: C 104 GLU cc_start: 0.8869 (tt0) cc_final: 0.8642 (tp30) REVERT: D 13 LYS cc_start: 0.9001 (tttt) cc_final: 0.8656 (ttmm) REVERT: D 42 GLU cc_start: 0.8329 (tt0) cc_final: 0.7517 (tm-30) REVERT: D 67 ASP cc_start: 0.8745 (t0) cc_final: 0.8374 (t0) REVERT: D 106 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5709 (mp) REVERT: D 189 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7760 (ttt180) REVERT: E 13 LYS cc_start: 0.8845 (tttt) cc_final: 0.8473 (ttmm) REVERT: E 39 THR cc_start: 0.8734 (m) cc_final: 0.8487 (m) REVERT: E 42 GLU cc_start: 0.8336 (tt0) cc_final: 0.7794 (tm-30) REVERT: E 47 ASP cc_start: 0.9084 (p0) cc_final: 0.8821 (p0) REVERT: E 101 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7669 (mtp-110) REVERT: E 103 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8096 (tm-30) REVERT: E 104 GLU cc_start: 0.9121 (tp30) cc_final: 0.8864 (tp30) REVERT: E 189 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7726 (ttt180) REVERT: F 13 LYS cc_start: 0.8959 (tttt) cc_final: 0.8646 (ttmm) REVERT: F 42 GLU cc_start: 0.8396 (tt0) cc_final: 0.7773 (tm-30) REVERT: F 55 ASN cc_start: 0.8849 (t0) cc_final: 0.8499 (t0) REVERT: H 13 LYS cc_start: 0.8999 (tttt) cc_final: 0.8650 (ttmm) REVERT: H 42 GLU cc_start: 0.8331 (tt0) cc_final: 0.7483 (tm-30) REVERT: H 106 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5587 (mp) REVERT: I 13 LYS cc_start: 0.8839 (tttt) cc_final: 0.8492 (ttmm) REVERT: I 42 GLU cc_start: 0.8375 (tt0) cc_final: 0.7700 (tm-30) REVERT: I 101 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7679 (mtp-110) REVERT: J 13 LYS cc_start: 0.8921 (tttt) cc_final: 0.8619 (ttmm) REVERT: J 42 GLU cc_start: 0.8399 (tt0) cc_final: 0.7779 (tm-30) REVERT: J 55 ASN cc_start: 0.8870 (t0) cc_final: 0.8523 (t0) REVERT: K 13 LYS cc_start: 0.9026 (tttt) cc_final: 0.8692 (ttmm) REVERT: K 17 TYR cc_start: 0.8728 (m-80) cc_final: 0.8367 (m-80) REVERT: K 42 GLU cc_start: 0.8428 (tt0) cc_final: 0.7617 (tm-30) REVERT: K 67 ASP cc_start: 0.8800 (t0) cc_final: 0.8504 (t0) REVERT: K 212 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7979 (t80) REVERT: L 13 LYS cc_start: 0.8855 (tttt) cc_final: 0.8513 (ttmm) REVERT: L 35 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8297 (tt) REVERT: L 39 THR cc_start: 0.8817 (m) cc_final: 0.8535 (m) REVERT: L 42 GLU cc_start: 0.8372 (tt0) cc_final: 0.7858 (tm-30) REVERT: L 47 ASP cc_start: 0.9089 (p0) cc_final: 0.8844 (p0) REVERT: L 67 ASP cc_start: 0.8882 (t0) cc_final: 0.8566 (t0) REVERT: L 101 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7766 (mtp-110) REVERT: L 103 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8184 (tm-30) REVERT: L 189 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7739 (ttt180) outliers start: 28 outliers final: 19 residues processed: 519 average time/residue: 0.1689 time to fit residues: 129.3423 Evaluate side-chains 514 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 491 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 218 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN A 81 GLN D 55 ASN F 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099612 restraints weight = 28928.981| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3085 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20184 Z= 0.106 Angle : 0.440 5.524 27360 Z= 0.236 Chirality : 0.033 0.169 3096 Planarity : 0.003 0.029 3300 Dihedral : 2.961 11.951 2592 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.20 % Allowed : 18.43 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.17), residues: 2364 helix: 3.41 (0.12), residues: 1680 sheet: 2.34 (0.46), residues: 132 loop : -1.79 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 101 TYR 0.018 0.001 TYR D 230 PHE 0.010 0.001 PHE A 32 TRP 0.003 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00232 (20148) covalent geometry : angle 0.43945 (27288) SS BOND : bond 0.00081 ( 36) SS BOND : angle 0.54377 ( 72) hydrogen bonds : bond 0.03556 ( 1368) hydrogen bonds : angle 2.56084 ( 4068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 498 time to evaluate : 0.974 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 13 LYS cc_start: 0.9023 (tttt) cc_final: 0.8643 (ttmm) REVERT: A 42 GLU cc_start: 0.8326 (tt0) cc_final: 0.7459 (tm-30) REVERT: A 67 ASP cc_start: 0.8694 (t0) cc_final: 0.8298 (t0) REVERT: A 103 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8321 (tm-30) REVERT: G 13 LYS cc_start: 0.8915 (tttt) cc_final: 0.8605 (ttmm) REVERT: G 15 GLN cc_start: 0.8943 (mt0) cc_final: 0.8698 (mt0) REVERT: G 42 GLU cc_start: 0.8537 (tt0) cc_final: 0.7771 (tm-30) REVERT: G 55 ASN cc_start: 0.8865 (t0) cc_final: 0.8543 (t0) REVERT: G 224 ASN cc_start: 0.8793 (m-40) cc_final: 0.8567 (m-40) REVERT: B 13 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: B 39 THR cc_start: 0.8828 (m) cc_final: 0.8596 (m) REVERT: B 42 GLU cc_start: 0.8360 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 47 ASP cc_start: 0.9097 (p0) cc_final: 0.8860 (p0) REVERT: B 101 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7719 (mtp-110) REVERT: B 153 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7915 (mtm180) REVERT: C 13 LYS cc_start: 0.8896 (tttt) cc_final: 0.8579 (ttmm) REVERT: C 42 GLU cc_start: 0.8519 (tt0) cc_final: 0.7880 (tm-30) REVERT: C 47 ASP cc_start: 0.9078 (p0) cc_final: 0.8815 (p0) REVERT: C 55 ASN cc_start: 0.8901 (t0) cc_final: 0.8582 (t0) REVERT: C 104 GLU cc_start: 0.8827 (tt0) cc_final: 0.8623 (tp30) REVERT: D 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8653 (ttmm) REVERT: D 42 GLU cc_start: 0.8284 (tt0) cc_final: 0.7467 (tm-30) REVERT: D 67 ASP cc_start: 0.8739 (t0) cc_final: 0.8390 (t0) REVERT: D 106 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5681 (mp) REVERT: E 13 LYS cc_start: 0.8834 (tttt) cc_final: 0.8486 (ttmm) REVERT: E 39 THR cc_start: 0.8763 (m) cc_final: 0.8515 (m) REVERT: E 42 GLU cc_start: 0.8353 (tt0) cc_final: 0.7810 (tm-30) REVERT: E 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8849 (p0) REVERT: E 101 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7657 (mtp-110) REVERT: E 104 GLU cc_start: 0.9115 (tp30) cc_final: 0.8868 (tp30) REVERT: E 189 ARG cc_start: 0.8071 (ttt180) cc_final: 0.7815 (ttt180) REVERT: F 13 LYS cc_start: 0.8904 (tttt) cc_final: 0.8616 (ttmm) REVERT: F 42 GLU cc_start: 0.8416 (tt0) cc_final: 0.7784 (tm-30) REVERT: F 55 ASN cc_start: 0.8863 (t0) cc_final: 0.8521 (t0) REVERT: H 13 LYS cc_start: 0.8980 (tttt) cc_final: 0.8616 (ttmm) REVERT: H 42 GLU cc_start: 0.8340 (tt0) cc_final: 0.7487 (tm-30) REVERT: H 106 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5622 (mp) REVERT: I 13 LYS cc_start: 0.8828 (tttt) cc_final: 0.8520 (ttmm) REVERT: I 42 GLU cc_start: 0.8399 (tt0) cc_final: 0.7720 (tm-30) REVERT: I 101 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7642 (mtp-110) REVERT: J 13 LYS cc_start: 0.8859 (tttt) cc_final: 0.8580 (ttmm) REVERT: J 42 GLU cc_start: 0.8408 (tt0) cc_final: 0.7787 (tm-30) REVERT: J 55 ASN cc_start: 0.8880 (t0) cc_final: 0.8553 (t0) REVERT: K 13 LYS cc_start: 0.8999 (tttt) cc_final: 0.8652 (ttmm) REVERT: K 17 TYR cc_start: 0.8726 (m-80) cc_final: 0.8370 (m-80) REVERT: K 42 GLU cc_start: 0.8378 (tt0) cc_final: 0.7556 (tm-30) REVERT: K 67 ASP cc_start: 0.8804 (t0) cc_final: 0.8490 (t0) REVERT: L 13 LYS cc_start: 0.8831 (tttt) cc_final: 0.8495 (ttmm) REVERT: L 35 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8300 (tt) REVERT: L 39 THR cc_start: 0.8827 (m) cc_final: 0.8548 (m) REVERT: L 42 GLU cc_start: 0.8365 (tt0) cc_final: 0.7817 (tm-30) REVERT: L 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8869 (p0) REVERT: L 67 ASP cc_start: 0.8907 (t0) cc_final: 0.8604 (t0) REVERT: L 101 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: L 189 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7802 (ttt180) REVERT: L 227 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8101 (mm-30) outliers start: 26 outliers final: 19 residues processed: 504 average time/residue: 0.1644 time to fit residues: 122.6232 Evaluate side-chains 517 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 495 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 217 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 81 GLN D 81 GLN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097353 restraints weight = 29047.991| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.52 r_work: 0.3038 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20184 Z= 0.125 Angle : 0.462 5.495 27360 Z= 0.249 Chirality : 0.034 0.160 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.028 12.723 2592 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 18.75 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.17), residues: 2364 helix: 3.44 (0.12), residues: 1680 sheet: 2.36 (0.46), residues: 132 loop : -1.78 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 53 TYR 0.025 0.001 TYR J 230 PHE 0.011 0.001 PHE H 32 TRP 0.004 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 Details of bonding type rmsd covalent geometry : bond 0.00288 (20148) covalent geometry : angle 0.46212 (27288) SS BOND : bond 0.00095 ( 36) SS BOND : angle 0.58482 ( 72) hydrogen bonds : bond 0.04031 ( 1368) hydrogen bonds : angle 2.62419 ( 4068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4010.38 seconds wall clock time: 69 minutes 40.76 seconds (4180.76 seconds total)