Starting phenix.real_space_refine on Tue Jun 17 05:23:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_33391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_33391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_33391.map" model { file = "/net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_33391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xq9_33391/06_2025/7xq9_33391.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 6.05, per 1000 atoms: 0.31 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 C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 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: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.85 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: 5.25 Time building geometry restraints manager: 5.38 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 0.740 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: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 36.850 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (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 TRP 0.011 0.001 TRP K 45 HIS 0.001 0.001 HIS I 194 PHE 0.021 0.002 PHE H 212 TYR 0.011 0.001 TYR G 66 ARG 0.002 0.000 ARG J 101 Details of bonding type rmsd hydrogen bonds : bond 0.14580 ( 1368) hydrogen bonds : angle 4.67326 ( 4068) SS BOND : bond 0.00195 ( 36) SS BOND : angle 0.92773 ( 72) covalent geometry : bond 0.00512 (20148) covalent geometry : angle 0.82634 (27288) *********************** 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 : 2.218 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: 0.8481 (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: 0.7365 (mt-10) cc_final: 0.6964 (tt0) REVERT: D 227 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8270 (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: 0.7341 (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: 0.7309 (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: 0.8280 (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: 0.3389 time to fit residues: 287.5649 Evaluate side-chains 470 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 202 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 194 HIS D 15 GLN H 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098547 restraints weight = 28824.666| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.55 r_work: 0.3073 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20184 Z= 0.118 Angle : 0.480 5.720 27360 Z= 0.258 Chirality : 0.034 0.130 3096 Planarity : 0.004 0.033 3300 Dihedral : 6.599 56.443 2654 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.18 % Allowed : 10.37 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2364 helix: 1.83 (0.12), residues: 1668 sheet: 2.02 (0.49), residues: 132 loop : -2.66 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.002 0.000 HIS B 194 PHE 0.012 0.001 PHE F 229 TYR 0.014 0.001 TYR E 230 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 1368) hydrogen bonds : angle 3.04563 ( 4068) SS BOND : bond 0.00096 ( 36) SS BOND : angle 0.69411 ( 72) covalent geometry : bond 0.00253 (20148) covalent geometry : angle 0.47887 (27288) *********************** 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 507 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 460 time to evaluate : 2.053 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 13 LYS cc_start: 0.8998 (tttt) cc_final: 0.8558 (ttmm) REVERT: A 17 TYR cc_start: 0.8782 (m-80) cc_final: 0.8453 (m-10) REVERT: A 42 GLU cc_start: 0.8422 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 67 ASP cc_start: 0.8613 (t0) cc_final: 0.8362 (t0) REVERT: A 100 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8241 (mtm) REVERT: A 230 TYR cc_start: 0.7699 (t80) cc_final: 0.7442 (t80) REVERT: G 13 LYS cc_start: 0.8916 (tttt) cc_final: 0.8563 (ttmm) REVERT: G 17 TYR cc_start: 0.8845 (m-80) cc_final: 0.8582 (m-80) REVERT: G 47 ASP cc_start: 0.9133 (p0) cc_final: 0.8921 (p0) REVERT: G 55 ASN cc_start: 0.8985 (t0) cc_final: 0.8638 (t0) REVERT: G 90 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8555 (mt) REVERT: G 101 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7582 (mtp-110) REVERT: B 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8591 (ttmm) REVERT: B 47 ASP cc_start: 0.9137 (p0) cc_final: 0.8895 (p0) REVERT: B 189 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7536 (ttm170) REVERT: C 13 LYS cc_start: 0.8933 (tttt) cc_final: 0.8543 (ttmm) REVERT: C 42 GLU cc_start: 0.8495 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 47 ASP cc_start: 0.9155 (p0) cc_final: 0.8897 (p0) REVERT: C 67 ASP cc_start: 0.8950 (t0) cc_final: 0.8711 (t0) REVERT: C 189 ARG cc_start: 0.7358 (ttt180) cc_final: 0.7129 (ttt180) REVERT: D 13 LYS cc_start: 0.9021 (tttt) cc_final: 0.8679 (ttmm) REVERT: D 227 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8390 (mm-30) REVERT: E 13 LYS cc_start: 0.8869 (tttt) cc_final: 0.8610 (ttmm) REVERT: E 42 GLU cc_start: 0.8368 (tt0) cc_final: 0.7840 (tm-30) REVERT: E 47 ASP cc_start: 0.9165 (p0) cc_final: 0.8940 (p0) REVERT: E 189 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7749 (ttm170) REVERT: F 13 LYS cc_start: 0.8884 (tttt) cc_final: 0.8558 (ttmm) REVERT: F 17 TYR cc_start: 0.8766 (m-80) cc_final: 0.8506 (m-80) REVERT: F 55 ASN cc_start: 0.8987 (t0) cc_final: 0.8648 (t0) REVERT: F 90 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8562 (mt) REVERT: H 17 TYR cc_start: 0.8732 (m-80) cc_final: 0.8421 (m-10) REVERT: H 227 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8427 (mm-30) REVERT: H 230 TYR cc_start: 0.7697 (t80) cc_final: 0.7395 (t80) REVERT: I 13 LYS cc_start: 0.8780 (tttt) cc_final: 0.8434 (ttmm) REVERT: J 13 LYS cc_start: 0.8898 (tttt) cc_final: 0.8554 (ttmm) REVERT: J 35 LEU cc_start: 0.8831 (tp) cc_final: 0.8612 (tt) REVERT: J 90 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8585 (mt) REVERT: J 227 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8305 (mm-30) REVERT: K 13 LYS cc_start: 0.8981 (tttt) cc_final: 0.8643 (ttmm) REVERT: K 42 GLU cc_start: 0.8343 (tt0) cc_final: 0.7718 (tm-30) REVERT: K 100 MET cc_start: 0.8650 (mtp) cc_final: 0.8404 (mtm) REVERT: L 13 LYS cc_start: 0.8909 (tttt) cc_final: 0.8569 (ttmm) REVERT: L 17 TYR cc_start: 0.8683 (m-80) cc_final: 0.8465 (m-80) REVERT: L 47 ASP cc_start: 0.9165 (p0) cc_final: 0.8952 (p0) REVERT: L 101 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7760 (mtp-110) REVERT: L 189 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7670 (ttm170) outliers start: 47 outliers final: 11 residues processed: 482 average time/residue: 0.3341 time to fit residues: 237.2694 Evaluate side-chains 447 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 432 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain L residue 7 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.093482 restraints weight = 29085.154| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.52 r_work: 0.3006 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 20184 Z= 0.189 Angle : 0.521 5.236 27360 Z= 0.281 Chirality : 0.036 0.131 3096 Planarity : 0.003 0.030 3300 Dihedral : 4.402 57.601 2602 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.01 % Allowed : 12.59 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.17), residues: 2364 helix: 2.49 (0.12), residues: 1668 sheet: 2.39 (0.48), residues: 132 loop : -2.36 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 45 HIS 0.003 0.001 HIS H 194 PHE 0.017 0.002 PHE L 169 TYR 0.018 0.001 TYR B 230 ARG 0.002 0.000 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 1368) hydrogen bonds : angle 3.03895 ( 4068) SS BOND : bond 0.00154 ( 36) SS BOND : angle 0.75890 ( 72) covalent geometry : bond 0.00445 (20148) covalent geometry : angle 0.52070 (27288) *********************** 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 509 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 444 time to evaluate : 2.308 Fit side-chains revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9081 (tttt) cc_final: 0.8649 (ttmm) REVERT: A 17 TYR cc_start: 0.8787 (m-80) cc_final: 0.8482 (m-10) REVERT: A 42 GLU cc_start: 0.8476 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 67 ASP cc_start: 0.8739 (t0) cc_final: 0.8427 (t0) REVERT: G 13 LYS cc_start: 0.8939 (tttt) cc_final: 0.8576 (ttmm) REVERT: G 17 TYR cc_start: 0.8840 (m-80) cc_final: 0.8584 (m-80) REVERT: G 55 ASN cc_start: 0.9115 (t0) cc_final: 0.8732 (t0) REVERT: B 13 LYS cc_start: 0.8926 (tttt) cc_final: 0.8594 (ttmm) REVERT: B 47 ASP cc_start: 0.9108 (p0) cc_final: 0.8870 (p0) REVERT: B 67 ASP cc_start: 0.8904 (t0) cc_final: 0.8701 (t0) REVERT: C 13 LYS cc_start: 0.8937 (tttt) cc_final: 0.8586 (ttmm) REVERT: C 35 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8508 (tp) REVERT: C 42 GLU cc_start: 0.8520 (tt0) cc_final: 0.7917 (tm-30) REVERT: C 47 ASP cc_start: 0.9139 (p0) cc_final: 0.8892 (p0) REVERT: D 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8559 (ttmm) REVERT: D 42 GLU cc_start: 0.8339 (tt0) cc_final: 0.7707 (tm-30) REVERT: D 67 ASP cc_start: 0.8682 (t0) cc_final: 0.8273 (t0) REVERT: D 106 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6096 (mp) REVERT: D 227 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8423 (mm-30) REVERT: E 13 LYS cc_start: 0.8939 (tttt) cc_final: 0.8518 (ttmm) REVERT: E 42 GLU cc_start: 0.8412 (tt0) cc_final: 0.7859 (tm-30) REVERT: E 47 ASP cc_start: 0.9118 (p0) cc_final: 0.8873 (p0) REVERT: E 67 ASP cc_start: 0.8849 (t0) cc_final: 0.8646 (t0) REVERT: E 189 ARG cc_start: 0.8477 (ttt180) cc_final: 0.7962 (ttm170) REVERT: F 13 LYS cc_start: 0.8915 (tttt) cc_final: 0.8573 (ttmm) REVERT: F 17 TYR cc_start: 0.8820 (m-80) cc_final: 0.8510 (m-80) REVERT: F 42 GLU cc_start: 0.8517 (tt0) cc_final: 0.7816 (tm-30) REVERT: F 55 ASN cc_start: 0.9133 (t0) cc_final: 0.8725 (t0) REVERT: H 13 LYS cc_start: 0.9000 (tttt) cc_final: 0.8619 (ttmm) REVERT: H 17 TYR cc_start: 0.8801 (m-80) cc_final: 0.8489 (m-10) REVERT: H 42 GLU cc_start: 0.8444 (tt0) cc_final: 0.7701 (tm-30) REVERT: H 106 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5985 (mp) REVERT: I 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8535 (ttmm) REVERT: I 17 TYR cc_start: 0.8755 (m-80) cc_final: 0.8535 (m-80) REVERT: J 13 LYS cc_start: 0.8906 (tttt) cc_final: 0.8587 (ttmm) REVERT: J 35 LEU cc_start: 0.8931 (tp) cc_final: 0.8671 (tt) REVERT: J 42 GLU cc_start: 0.8491 (tt0) cc_final: 0.7802 (tm-30) REVERT: K 13 LYS cc_start: 0.9014 (tttt) cc_final: 0.8685 (ttmm) REVERT: K 42 GLU cc_start: 0.8435 (tt0) cc_final: 0.7691 (tm-30) REVERT: K 55 ASN cc_start: 0.9114 (t0) cc_final: 0.8914 (t0) REVERT: K 67 ASP cc_start: 0.8706 (t0) cc_final: 0.8371 (t0) REVERT: K 100 MET cc_start: 0.8572 (mtp) cc_final: 0.8331 (mtm) REVERT: K 189 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8144 (ttm170) REVERT: K 212 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8139 (t80) REVERT: L 13 LYS cc_start: 0.8913 (tttt) cc_final: 0.8540 (ttmm) REVERT: L 17 TYR cc_start: 0.8691 (m-80) cc_final: 0.8481 (m-80) REVERT: L 42 GLU cc_start: 0.8446 (tt0) cc_final: 0.7724 (tm-30) REVERT: L 47 ASP cc_start: 0.9142 (p0) cc_final: 0.8933 (p0) REVERT: L 101 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7804 (mtp-110) outliers start: 65 outliers final: 37 residues processed: 475 average time/residue: 0.3409 time to fit residues: 239.1052 Evaluate side-chains 468 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 427 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain B residue 7 LEU 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 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 99 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 164 ILE 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 212 PHE Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 34 ILE 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 35 LEU 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 104 optimal weight: 0.4980 chunk 108 optimal weight: 0.0570 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.129505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098758 restraints weight = 28854.037| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3095 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2267 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= 0.105 Angle : 0.430 5.386 27360 Z= 0.233 Chirality : 0.034 0.141 3096 Planarity : 0.003 0.031 3300 Dihedral : 3.355 13.597 2592 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.11 % Allowed : 16.02 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.17), residues: 2364 helix: 2.85 (0.12), residues: 1668 sheet: 2.32 (0.47), residues: 132 loop : -2.27 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 45 HIS 0.001 0.000 HIS E 194 PHE 0.010 0.001 PHE A 32 TYR 0.019 0.001 TYR H 230 ARG 0.002 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1368) hydrogen bonds : angle 2.74778 ( 4068) SS BOND : bond 0.00151 ( 36) SS BOND : angle 0.70396 ( 72) covalent geometry : bond 0.00212 (20148) covalent geometry : angle 0.42954 (27288) *********************** 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 504 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 2.353 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: 0.9046 (tttt) cc_final: 0.8669 (ttmm) REVERT: A 17 TYR cc_start: 0.8749 (m-80) cc_final: 0.8541 (m-80) REVERT: A 42 GLU cc_start: 0.8392 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 67 ASP cc_start: 0.8654 (t0) cc_final: 0.8320 (t0) REVERT: G 13 LYS cc_start: 0.8962 (tttt) cc_final: 0.8615 (ttmm) REVERT: G 42 GLU cc_start: 0.8421 (tt0) cc_final: 0.7670 (tm-30) REVERT: G 55 ASN cc_start: 0.8954 (t0) cc_final: 0.8608 (t0) REVERT: B 13 LYS cc_start: 0.8916 (tttt) cc_final: 0.8587 (ttmm) REVERT: B 42 GLU cc_start: 0.8402 (tt0) cc_final: 0.7793 (tm-30) REVERT: B 47 ASP cc_start: 0.9068 (p0) cc_final: 0.8811 (p0) REVERT: B 67 ASP cc_start: 0.8859 (t0) cc_final: 0.8649 (t0) REVERT: B 169 PHE cc_start: 0.8599 (m-80) cc_final: 0.8383 (m-10) REVERT: C 13 LYS cc_start: 0.8954 (tttt) cc_final: 0.8609 (ttmm) REVERT: C 42 GLU cc_start: 0.8471 (tt0) cc_final: 0.7909 (tm-30) REVERT: C 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8859 (p0) REVERT: D 13 LYS cc_start: 0.8968 (tttt) cc_final: 0.8616 (ttmm) REVERT: D 42 GLU cc_start: 0.8281 (tt0) cc_final: 0.7729 (tm-30) REVERT: D 67 ASP cc_start: 0.8630 (t0) cc_final: 0.8361 (t0) REVERT: D 106 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6111 (mp) REVERT: D 227 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 13 LYS cc_start: 0.8966 (tttt) cc_final: 0.8596 (ttmm) REVERT: E 42 GLU cc_start: 0.8302 (tt0) cc_final: 0.7818 (tm-30) REVERT: E 47 ASP cc_start: 0.9080 (p0) cc_final: 0.8826 (p0) REVERT: E 101 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7740 (mtp-110) REVERT: E 189 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7632 (ttm170) REVERT: F 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8583 (ttmm) REVERT: F 42 GLU cc_start: 0.8440 (tt0) cc_final: 0.7754 (tm-30) REVERT: F 55 ASN cc_start: 0.9005 (t0) cc_final: 0.8679 (t0) REVERT: H 13 LYS cc_start: 0.8980 (tttt) cc_final: 0.8612 (ttmm) REVERT: H 42 GLU cc_start: 0.8454 (tt0) cc_final: 0.7774 (tm-30) REVERT: H 106 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5989 (mp) REVERT: H 189 ARG cc_start: 0.7828 (ttt180) cc_final: 0.7508 (ttt180) REVERT: I 13 LYS cc_start: 0.8910 (tttt) cc_final: 0.8510 (ttmm) REVERT: J 13 LYS cc_start: 0.8891 (tttt) cc_final: 0.8591 (ttmm) REVERT: J 42 GLU cc_start: 0.8492 (tt0) cc_final: 0.7792 (tm-30) REVERT: J 55 ASN cc_start: 0.8963 (t0) cc_final: 0.8648 (t0) REVERT: K 13 LYS cc_start: 0.9009 (tttt) cc_final: 0.8660 (ttmm) REVERT: K 42 GLU cc_start: 0.8506 (tt0) cc_final: 0.7671 (tm-30) REVERT: K 67 ASP cc_start: 0.8707 (t0) cc_final: 0.8462 (t0) REVERT: K 212 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (t80) REVERT: K 227 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8453 (mm-30) REVERT: L 13 LYS cc_start: 0.8928 (tttt) cc_final: 0.8555 (ttmm) REVERT: L 42 GLU cc_start: 0.8308 (tt0) cc_final: 0.7798 (tm-30) REVERT: L 47 ASP cc_start: 0.9087 (p0) cc_final: 0.8861 (p0) REVERT: L 101 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7735 (mtp-110) REVERT: L 189 ARG cc_start: 0.8009 (ttt180) cc_final: 0.7674 (ttt180) outliers start: 24 outliers final: 14 residues processed: 487 average time/residue: 0.3308 time to fit residues: 238.3332 Evaluate side-chains 471 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 454 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU 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 35 LEU Chi-restraints excluded: chain F residue 212 PHE 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 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 212 PHE 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 153 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 195 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 33 optimal weight: 0.0670 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097848 restraints weight = 29137.987| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.56 r_work: 0.3074 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20184 Z= 0.112 Angle : 0.434 5.425 27360 Z= 0.235 Chirality : 0.034 0.146 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.197 13.015 2592 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 16.99 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.17), residues: 2364 helix: 3.03 (0.12), residues: 1668 sheet: 2.37 (0.47), residues: 132 loop : -2.14 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE A 32 TYR 0.019 0.001 TYR J 230 ARG 0.003 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1368) hydrogen bonds : angle 2.68939 ( 4068) SS BOND : bond 0.00082 ( 36) SS BOND : angle 0.55587 ( 72) covalent geometry : bond 0.00247 (20148) covalent geometry : angle 0.43397 (27288) *********************** 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 504 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 475 time to evaluate : 2.338 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: 0.9052 (tttt) cc_final: 0.8686 (ttmm) REVERT: A 42 GLU cc_start: 0.8425 (tt0) cc_final: 0.7746 (tm-30) REVERT: A 67 ASP cc_start: 0.8668 (t0) cc_final: 0.8306 (t0) REVERT: G 13 LYS cc_start: 0.8941 (tttt) cc_final: 0.8603 (ttmm) REVERT: G 42 GLU cc_start: 0.8432 (tt0) cc_final: 0.7693 (tm-30) REVERT: G 55 ASN cc_start: 0.8999 (t0) cc_final: 0.8646 (t0) REVERT: B 13 LYS cc_start: 0.8879 (tttt) cc_final: 0.8555 (ttmm) REVERT: B 42 GLU cc_start: 0.8343 (tt0) cc_final: 0.7703 (tm-30) REVERT: B 47 ASP cc_start: 0.9086 (p0) cc_final: 0.8847 (p0) REVERT: B 67 ASP cc_start: 0.8882 (t0) cc_final: 0.8649 (t0) REVERT: C 13 LYS cc_start: 0.8960 (tttt) cc_final: 0.8615 (ttmm) REVERT: C 42 GLU cc_start: 0.8495 (tt0) cc_final: 0.7925 (tm-30) REVERT: C 47 ASP cc_start: 0.9111 (p0) cc_final: 0.8854 (p0) REVERT: C 55 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8690 (t0) REVERT: D 13 LYS cc_start: 0.8980 (tttt) cc_final: 0.8618 (ttmm) REVERT: D 42 GLU cc_start: 0.8326 (tt0) cc_final: 0.7760 (tm-30) REVERT: D 67 ASP cc_start: 0.8656 (t0) cc_final: 0.8384 (t0) REVERT: D 106 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6017 (mp) REVERT: D 227 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8467 (mm-30) REVERT: E 13 LYS cc_start: 0.8939 (tttt) cc_final: 0.8561 (ttmm) REVERT: E 42 GLU cc_start: 0.8321 (tt0) cc_final: 0.7843 (tm-30) REVERT: E 47 ASP cc_start: 0.9090 (p0) cc_final: 0.8842 (p0) REVERT: E 101 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7722 (mtp-110) REVERT: E 189 ARG cc_start: 0.8157 (ttt180) cc_final: 0.7658 (ttm170) REVERT: F 13 LYS cc_start: 0.8900 (tttt) cc_final: 0.8592 (ttmm) REVERT: F 42 GLU cc_start: 0.8408 (tt0) cc_final: 0.7745 (tm-30) REVERT: F 55 ASN cc_start: 0.9008 (t0) cc_final: 0.8648 (t0) REVERT: H 13 LYS cc_start: 0.8994 (tttt) cc_final: 0.8622 (ttmm) REVERT: H 35 LEU cc_start: 0.8798 (tp) cc_final: 0.8577 (tt) REVERT: H 42 GLU cc_start: 0.8324 (tt0) cc_final: 0.7579 (tm-30) REVERT: H 106 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5954 (mp) REVERT: I 13 LYS cc_start: 0.8895 (tttt) cc_final: 0.8544 (ttmm) REVERT: I 101 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7617 (mtp-110) REVERT: J 13 LYS cc_start: 0.8891 (tttt) cc_final: 0.8592 (ttmm) REVERT: J 42 GLU cc_start: 0.8450 (tt0) cc_final: 0.7763 (tm-30) REVERT: J 55 ASN cc_start: 0.8982 (t0) cc_final: 0.8634 (t0) REVERT: K 13 LYS cc_start: 0.9011 (tttt) cc_final: 0.8634 (ttmm) REVERT: K 42 GLU cc_start: 0.8469 (tt0) cc_final: 0.7650 (tm-30) REVERT: K 67 ASP cc_start: 0.8670 (t0) cc_final: 0.8408 (t0) REVERT: K 103 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8307 (tm-30) REVERT: K 212 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8045 (t80) REVERT: L 13 LYS cc_start: 0.8881 (tttt) cc_final: 0.8522 (ttmm) REVERT: L 42 GLU cc_start: 0.8342 (tt0) cc_final: 0.7826 (tm-30) REVERT: L 47 ASP cc_start: 0.9097 (p0) cc_final: 0.8840 (p0) REVERT: L 101 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7704 (mtp-110) REVERT: L 189 ARG cc_start: 0.8169 (ttt180) cc_final: 0.7839 (ttt180) outliers start: 29 outliers final: 17 residues processed: 486 average time/residue: 0.3379 time to fit residues: 242.0100 Evaluate side-chains 485 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 464 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 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 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 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 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 208 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN I 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096942 restraints weight = 29107.124| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.53 r_work: 0.3042 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20184 Z= 0.132 Angle : 0.456 5.411 27360 Z= 0.246 Chirality : 0.034 0.149 3096 Planarity : 0.003 0.031 3300 Dihedral : 3.204 12.589 2592 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.76 % Allowed : 17.18 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.17), residues: 2364 helix: 3.13 (0.12), residues: 1668 sheet: 2.37 (0.47), residues: 132 loop : -2.08 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 PHE 0.012 0.001 PHE A 32 TYR 0.012 0.001 TYR J 66 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 1368) hydrogen bonds : angle 2.70392 ( 4068) SS BOND : bond 0.00115 ( 36) SS BOND : angle 0.65432 ( 72) covalent geometry : bond 0.00305 (20148) covalent geometry : angle 0.45493 (27288) *********************** 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 501 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 463 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9061 (tttt) cc_final: 0.8726 (ttmm) REVERT: A 42 GLU cc_start: 0.8348 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 67 ASP cc_start: 0.8719 (t0) cc_final: 0.8365 (t0) REVERT: G 13 LYS cc_start: 0.8937 (tttt) cc_final: 0.8635 (ttmm) REVERT: G 42 GLU cc_start: 0.8446 (tt0) cc_final: 0.7744 (tm-30) REVERT: G 55 ASN cc_start: 0.9071 (t0) cc_final: 0.8709 (t0) REVERT: B 13 LYS cc_start: 0.8892 (tttt) cc_final: 0.8548 (ttmm) REVERT: B 42 GLU cc_start: 0.8335 (tt0) cc_final: 0.7690 (tm-30) REVERT: B 47 ASP cc_start: 0.9091 (p0) cc_final: 0.8854 (p0) REVERT: B 67 ASP cc_start: 0.8913 (t0) cc_final: 0.8689 (t0) REVERT: C 13 LYS cc_start: 0.8944 (tttt) cc_final: 0.8619 (ttmm) REVERT: C 42 GLU cc_start: 0.8532 (tt0) cc_final: 0.7915 (tm-30) REVERT: C 47 ASP cc_start: 0.9113 (p0) cc_final: 0.8860 (p0) REVERT: D 13 LYS cc_start: 0.8978 (tttt) cc_final: 0.8612 (ttmm) REVERT: D 42 GLU cc_start: 0.8380 (tt0) cc_final: 0.7726 (tm-30) REVERT: D 67 ASP cc_start: 0.8700 (t0) cc_final: 0.8306 (t0) REVERT: D 106 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5895 (mp) REVERT: D 227 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8404 (mm-30) REVERT: E 13 LYS cc_start: 0.8845 (tttt) cc_final: 0.8464 (ttmm) REVERT: E 42 GLU cc_start: 0.8320 (tt0) cc_final: 0.7824 (tm-30) REVERT: E 47 ASP cc_start: 0.9109 (p0) cc_final: 0.8862 (p0) REVERT: E 101 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7698 (mtp-110) REVERT: F 13 LYS cc_start: 0.8900 (tttt) cc_final: 0.8600 (ttmm) REVERT: F 42 GLU cc_start: 0.8405 (tt0) cc_final: 0.7715 (tm-30) REVERT: F 55 ASN cc_start: 0.9072 (t0) cc_final: 0.8705 (t0) REVERT: H 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8617 (ttmm) REVERT: H 42 GLU cc_start: 0.8361 (tt0) cc_final: 0.7543 (tm-30) REVERT: H 106 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5971 (mp) REVERT: I 13 LYS cc_start: 0.8863 (tttt) cc_final: 0.8522 (ttmm) REVERT: I 42 GLU cc_start: 0.8415 (tt0) cc_final: 0.7690 (tm-30) REVERT: I 101 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7633 (mtp-110) REVERT: J 13 LYS cc_start: 0.8876 (tttt) cc_final: 0.8564 (ttmm) REVERT: J 42 GLU cc_start: 0.8380 (tt0) cc_final: 0.7718 (tm-30) REVERT: J 55 ASN cc_start: 0.9056 (t0) cc_final: 0.8689 (t0) REVERT: K 13 LYS cc_start: 0.8995 (tttt) cc_final: 0.8675 (ttmm) REVERT: K 42 GLU cc_start: 0.8425 (tt0) cc_final: 0.7600 (tm-30) REVERT: K 67 ASP cc_start: 0.8707 (t0) cc_final: 0.8495 (t0) REVERT: K 212 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8090 (t80) REVERT: L 13 LYS cc_start: 0.8862 (tttt) cc_final: 0.8511 (ttmm) REVERT: L 42 GLU cc_start: 0.8341 (tt0) cc_final: 0.7821 (tm-30) REVERT: L 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8862 (p0) REVERT: L 101 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7754 (mtp-110) REVERT: L 189 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7864 (ttt180) outliers start: 38 outliers final: 27 residues processed: 477 average time/residue: 0.3554 time to fit residues: 247.7075 Evaluate side-chains 485 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 455 time to evaluate : 2.446 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 35 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 19 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 228 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 106 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 11 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 107 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 107 ASN 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 130 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN F 15 GLN H 55 ASN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098872 restraints weight = 28786.123| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.54 r_work: 0.3099 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2647 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= 0.106 Angle : 0.435 6.237 27360 Z= 0.235 Chirality : 0.033 0.153 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.099 12.957 2592 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.53 % Allowed : 17.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.17), residues: 2364 helix: 3.25 (0.12), residues: 1668 sheet: 2.33 (0.47), residues: 132 loop : -2.05 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 45 HIS 0.001 0.000 HIS L 74 PHE 0.011 0.001 PHE A 32 TYR 0.020 0.001 TYR F 230 ARG 0.004 0.000 ARG K 101 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1368) hydrogen bonds : angle 2.62319 ( 4068) SS BOND : bond 0.00076 ( 36) SS BOND : angle 0.55538 ( 72) covalent geometry : bond 0.00227 (20148) covalent geometry : angle 0.43458 (27288) *********************** 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 515 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 482 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9081 (tttt) cc_final: 0.8738 (ttmm) REVERT: A 42 GLU cc_start: 0.8289 (tt0) cc_final: 0.7504 (tm-30) REVERT: A 67 ASP cc_start: 0.8678 (t0) cc_final: 0.8279 (t0) REVERT: G 13 LYS cc_start: 0.8979 (tttt) cc_final: 0.8658 (ttmm) REVERT: G 15 GLN cc_start: 0.8881 (mt0) cc_final: 0.8627 (mt0) REVERT: G 42 GLU cc_start: 0.8420 (tt0) cc_final: 0.7741 (tm-30) REVERT: G 55 ASN cc_start: 0.8973 (t0) cc_final: 0.8623 (t0) REVERT: B 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8545 (ttmm) REVERT: B 39 THR cc_start: 0.8915 (m) cc_final: 0.8683 (m) REVERT: B 42 GLU cc_start: 0.8330 (tt0) cc_final: 0.7679 (tm-30) REVERT: B 47 ASP cc_start: 0.9085 (p0) cc_final: 0.8846 (p0) REVERT: B 67 ASP cc_start: 0.8907 (t0) cc_final: 0.8671 (t0) REVERT: C 13 LYS cc_start: 0.8956 (tttt) cc_final: 0.8623 (ttmm) REVERT: C 42 GLU cc_start: 0.8458 (tt0) cc_final: 0.7842 (tm-30) REVERT: C 47 ASP cc_start: 0.9121 (p0) cc_final: 0.8864 (p0) REVERT: D 13 LYS cc_start: 0.8998 (tttt) cc_final: 0.8622 (ttmm) REVERT: D 42 GLU cc_start: 0.8372 (tt0) cc_final: 0.7701 (tm-30) REVERT: D 67 ASP cc_start: 0.8668 (t0) cc_final: 0.8280 (t0) REVERT: D 106 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6052 (mp) REVERT: D 227 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 13 LYS cc_start: 0.8894 (tttt) cc_final: 0.8489 (ttmm) REVERT: E 39 THR cc_start: 0.8834 (m) cc_final: 0.8603 (m) REVERT: E 42 GLU cc_start: 0.8295 (tt0) cc_final: 0.7820 (tm-30) REVERT: E 47 ASP cc_start: 0.9070 (p0) cc_final: 0.8829 (p0) REVERT: E 101 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7775 (mtp-110) REVERT: F 13 LYS cc_start: 0.8910 (tttt) cc_final: 0.8608 (ttmm) REVERT: F 42 GLU cc_start: 0.8402 (tt0) cc_final: 0.7712 (tm-30) REVERT: F 55 ASN cc_start: 0.8989 (t0) cc_final: 0.8613 (t0) REVERT: H 13 LYS cc_start: 0.8999 (tttt) cc_final: 0.8614 (ttmm) REVERT: H 42 GLU cc_start: 0.8335 (tt0) cc_final: 0.7522 (tm-30) REVERT: H 106 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6044 (mp) REVERT: I 13 LYS cc_start: 0.8879 (tttt) cc_final: 0.8523 (ttmm) REVERT: I 42 GLU cc_start: 0.8360 (tt0) cc_final: 0.7668 (tm-30) REVERT: I 101 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7590 (mtp-110) REVERT: J 13 LYS cc_start: 0.8888 (tttt) cc_final: 0.8568 (ttmm) REVERT: J 42 GLU cc_start: 0.8389 (tt0) cc_final: 0.7713 (tm-30) REVERT: J 55 ASN cc_start: 0.8944 (t0) cc_final: 0.8585 (t0) REVERT: K 13 LYS cc_start: 0.8996 (tttt) cc_final: 0.8671 (ttmm) REVERT: K 42 GLU cc_start: 0.8410 (tt0) cc_final: 0.7581 (tm-30) REVERT: K 67 ASP cc_start: 0.8693 (t0) cc_final: 0.8472 (t0) REVERT: K 212 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8067 (t80) REVERT: L 13 LYS cc_start: 0.8872 (tttt) cc_final: 0.8510 (ttmm) REVERT: L 42 GLU cc_start: 0.8304 (tt0) cc_final: 0.7811 (tm-30) REVERT: L 47 ASP cc_start: 0.9091 (p0) cc_final: 0.8844 (p0) REVERT: L 101 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7753 (mtp-110) REVERT: L 189 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7825 (ttt180) outliers start: 33 outliers final: 30 residues processed: 493 average time/residue: 0.3498 time to fit residues: 253.6815 Evaluate side-chains 506 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 473 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 19 THR 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 212 PHE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 87 VAL 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 55 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 11 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 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.129832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099320 restraints weight = 28921.744| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.54 r_work: 0.3104 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2730 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= 0.105 Angle : 0.435 5.547 27360 Z= 0.235 Chirality : 0.033 0.164 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.064 13.069 2592 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 17.92 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.17), residues: 2364 helix: 3.24 (0.12), residues: 1680 sheet: 2.29 (0.46), residues: 132 loop : -1.96 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 PHE 0.013 0.001 PHE B 169 TYR 0.023 0.001 TYR I 230 ARG 0.004 0.000 ARG K 101 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1368) hydrogen bonds : angle 2.59405 ( 4068) SS BOND : bond 0.00080 ( 36) SS BOND : angle 0.54034 ( 72) covalent geometry : bond 0.00226 (20148) covalent geometry : angle 0.43428 (27288) *********************** 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 516 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 484 time to evaluate : 2.303 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 13 LYS cc_start: 0.9073 (tttt) cc_final: 0.8751 (ttmm) REVERT: A 42 GLU cc_start: 0.8228 (tt0) cc_final: 0.7536 (tm-30) REVERT: A 67 ASP cc_start: 0.8679 (t0) cc_final: 0.8286 (t0) REVERT: G 13 LYS cc_start: 0.8980 (tttt) cc_final: 0.8660 (ttmm) REVERT: G 15 GLN cc_start: 0.8875 (mt0) cc_final: 0.8626 (mt0) REVERT: G 42 GLU cc_start: 0.8463 (tt0) cc_final: 0.7738 (tm-30) REVERT: G 55 ASN cc_start: 0.8959 (t0) cc_final: 0.8614 (t0) REVERT: B 13 LYS cc_start: 0.8887 (tttt) cc_final: 0.8529 (ttmm) REVERT: B 39 THR cc_start: 0.8889 (m) cc_final: 0.8653 (m) REVERT: B 42 GLU cc_start: 0.8319 (tt0) cc_final: 0.7673 (tm-30) REVERT: B 47 ASP cc_start: 0.9090 (p0) cc_final: 0.8851 (p0) REVERT: B 67 ASP cc_start: 0.8900 (t0) cc_final: 0.8672 (t0) REVERT: B 101 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7768 (mtp-110) REVERT: B 230 TYR cc_start: 0.7728 (t80) cc_final: 0.7395 (t80) REVERT: C 13 LYS cc_start: 0.8949 (tttt) cc_final: 0.8610 (ttmm) REVERT: C 42 GLU cc_start: 0.8458 (tt0) cc_final: 0.7849 (tm-30) REVERT: C 47 ASP cc_start: 0.9063 (p0) cc_final: 0.8795 (p0) REVERT: C 55 ASN cc_start: 0.8817 (t0) cc_final: 0.8573 (t0) REVERT: D 13 LYS cc_start: 0.9001 (tttt) cc_final: 0.8668 (ttmm) REVERT: D 42 GLU cc_start: 0.8406 (tt0) cc_final: 0.7665 (tm-30) REVERT: D 67 ASP cc_start: 0.8678 (t0) cc_final: 0.8284 (t0) REVERT: D 106 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5943 (mp) REVERT: D 227 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8323 (mm-30) REVERT: E 13 LYS cc_start: 0.8849 (tttt) cc_final: 0.8463 (ttmm) REVERT: E 39 THR cc_start: 0.8811 (m) cc_final: 0.8578 (m) REVERT: E 42 GLU cc_start: 0.8336 (tt0) cc_final: 0.7782 (tm-30) REVERT: E 47 ASP cc_start: 0.9079 (p0) cc_final: 0.8841 (p0) REVERT: E 101 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7769 (mtp-110) REVERT: E 227 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7944 (mm-30) REVERT: F 13 LYS cc_start: 0.8911 (tttt) cc_final: 0.8606 (ttmm) REVERT: F 42 GLU cc_start: 0.8420 (tt0) cc_final: 0.7747 (tm-30) REVERT: F 55 ASN cc_start: 0.8960 (t0) cc_final: 0.8603 (t0) REVERT: H 13 LYS cc_start: 0.9005 (tttt) cc_final: 0.8619 (ttmm) REVERT: H 42 GLU cc_start: 0.8402 (tt0) cc_final: 0.7533 (tm-30) REVERT: H 106 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6054 (mp) REVERT: I 13 LYS cc_start: 0.8869 (tttt) cc_final: 0.8512 (ttmm) REVERT: I 42 GLU cc_start: 0.8365 (tt0) cc_final: 0.7673 (tm-30) REVERT: I 101 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7586 (mtp-110) REVERT: J 13 LYS cc_start: 0.8906 (tttt) cc_final: 0.8608 (ttmm) REVERT: J 42 GLU cc_start: 0.8384 (tt0) cc_final: 0.7716 (tm-30) REVERT: J 55 ASN cc_start: 0.8888 (t0) cc_final: 0.8527 (t0) REVERT: K 13 LYS cc_start: 0.8994 (tttt) cc_final: 0.8674 (ttmm) REVERT: K 42 GLU cc_start: 0.8412 (tt0) cc_final: 0.7610 (tm-30) REVERT: K 67 ASP cc_start: 0.8694 (t0) cc_final: 0.8483 (t0) REVERT: L 13 LYS cc_start: 0.8871 (tttt) cc_final: 0.8499 (ttmm) REVERT: L 39 THR cc_start: 0.8862 (m) cc_final: 0.8624 (m) REVERT: L 42 GLU cc_start: 0.8304 (tt0) cc_final: 0.7825 (tm-30) REVERT: L 47 ASP cc_start: 0.9089 (p0) cc_final: 0.8844 (p0) REVERT: L 101 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7740 (mtp-110) REVERT: L 189 ARG cc_start: 0.8086 (ttt180) cc_final: 0.7812 (ttt180) outliers start: 32 outliers final: 26 residues processed: 494 average time/residue: 0.3558 time to fit residues: 257.6091 Evaluate side-chains 510 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 482 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 35 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 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 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 87 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 0.0010 chunk 172 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099320 restraints weight = 28911.378| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.54 r_work: 0.3078 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20184 Z= 0.108 Angle : 0.441 5.500 27360 Z= 0.238 Chirality : 0.033 0.163 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.011 12.901 2592 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.34 % Allowed : 18.47 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.17), residues: 2364 helix: 3.32 (0.12), residues: 1680 sheet: 2.30 (0.46), residues: 132 loop : -1.88 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE B 169 TYR 0.023 0.001 TYR J 230 ARG 0.004 0.000 ARG K 101 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1368) hydrogen bonds : angle 2.58335 ( 4068) SS BOND : bond 0.00081 ( 36) SS BOND : angle 0.54056 ( 72) covalent geometry : bond 0.00237 (20148) covalent geometry : angle 0.44074 (27288) *********************** 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 517 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 488 time to evaluate : 2.131 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 13 LYS cc_start: 0.9064 (tttt) cc_final: 0.8734 (ttmm) REVERT: A 42 GLU cc_start: 0.8223 (tt0) cc_final: 0.7522 (tm-30) REVERT: A 67 ASP cc_start: 0.8696 (t0) cc_final: 0.8311 (t0) REVERT: G 13 LYS cc_start: 0.8942 (tttt) cc_final: 0.8628 (ttmm) REVERT: G 15 GLN cc_start: 0.8915 (mt0) cc_final: 0.8640 (mt0) REVERT: G 42 GLU cc_start: 0.8530 (tt0) cc_final: 0.7754 (tm-30) REVERT: G 55 ASN cc_start: 0.8899 (t0) cc_final: 0.8573 (t0) REVERT: B 13 LYS cc_start: 0.8865 (tttt) cc_final: 0.8539 (ttmm) REVERT: B 39 THR cc_start: 0.8875 (m) cc_final: 0.8638 (m) REVERT: B 42 GLU cc_start: 0.8313 (tt0) cc_final: 0.7674 (tm-30) REVERT: B 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8866 (p0) REVERT: B 67 ASP cc_start: 0.8917 (t0) cc_final: 0.8698 (t0) REVERT: B 101 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7721 (mtp-110) REVERT: C 13 LYS cc_start: 0.8892 (tttt) cc_final: 0.8568 (ttmm) REVERT: C 42 GLU cc_start: 0.8492 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 47 ASP cc_start: 0.9078 (p0) cc_final: 0.8818 (p0) REVERT: C 55 ASN cc_start: 0.8918 (t0) cc_final: 0.8611 (t0) REVERT: C 104 GLU cc_start: 0.8921 (tt0) cc_final: 0.8691 (tp30) REVERT: D 13 LYS cc_start: 0.8983 (tttt) cc_final: 0.8647 (ttmm) REVERT: D 42 GLU cc_start: 0.8218 (tt0) cc_final: 0.7463 (tm-30) REVERT: D 67 ASP cc_start: 0.8696 (t0) cc_final: 0.8297 (t0) REVERT: D 106 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5928 (mp) REVERT: D 227 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8445 (mm-30) REVERT: E 13 LYS cc_start: 0.8821 (tttt) cc_final: 0.8443 (ttmm) REVERT: E 39 THR cc_start: 0.8793 (m) cc_final: 0.8559 (m) REVERT: E 42 GLU cc_start: 0.8345 (tt0) cc_final: 0.7791 (tm-30) REVERT: E 47 ASP cc_start: 0.9095 (p0) cc_final: 0.8859 (p0) REVERT: E 101 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7759 (mtp-110) REVERT: E 227 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 13 LYS cc_start: 0.8893 (tttt) cc_final: 0.8594 (ttmm) REVERT: F 42 GLU cc_start: 0.8434 (tt0) cc_final: 0.7767 (tm-30) REVERT: F 55 ASN cc_start: 0.8928 (t0) cc_final: 0.8562 (t0) REVERT: H 13 LYS cc_start: 0.9005 (tttt) cc_final: 0.8645 (ttmm) REVERT: H 42 GLU cc_start: 0.8335 (tt0) cc_final: 0.7486 (tm-30) REVERT: H 106 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6035 (mp) REVERT: I 13 LYS cc_start: 0.8829 (tttt) cc_final: 0.8488 (ttmm) REVERT: I 42 GLU cc_start: 0.8341 (tt0) cc_final: 0.7672 (tm-30) REVERT: I 101 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7560 (mtp-110) REVERT: J 13 LYS cc_start: 0.8925 (tttt) cc_final: 0.8642 (ttmm) REVERT: J 42 GLU cc_start: 0.8399 (tt0) cc_final: 0.7752 (tm-30) REVERT: J 55 ASN cc_start: 0.8898 (t0) cc_final: 0.8533 (t0) REVERT: K 13 LYS cc_start: 0.9001 (tttt) cc_final: 0.8673 (ttmm) REVERT: K 42 GLU cc_start: 0.8437 (tt0) cc_final: 0.7610 (tm-30) REVERT: K 67 ASP cc_start: 0.8738 (t0) cc_final: 0.8534 (t0) REVERT: L 13 LYS cc_start: 0.8832 (tttt) cc_final: 0.8495 (ttmm) REVERT: L 39 THR cc_start: 0.8851 (m) cc_final: 0.8611 (m) REVERT: L 42 GLU cc_start: 0.8387 (tt0) cc_final: 0.7833 (tm-30) REVERT: L 47 ASP cc_start: 0.9095 (p0) cc_final: 0.8853 (p0) REVERT: L 101 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7714 (mtp-110) REVERT: L 189 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7832 (ttt180) outliers start: 29 outliers final: 25 residues processed: 497 average time/residue: 0.3451 time to fit residues: 250.7535 Evaluate side-chains 506 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 479 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 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 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 87 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.129835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099166 restraints weight = 28772.448| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.53 r_work: 0.3072 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20184 Z= 0.110 Angle : 0.446 5.495 27360 Z= 0.240 Chirality : 0.034 0.161 3096 Planarity : 0.003 0.029 3300 Dihedral : 2.997 12.876 2592 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.44 % Allowed : 18.01 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.17), residues: 2364 helix: 3.38 (0.12), residues: 1680 sheet: 2.31 (0.46), residues: 132 loop : -1.84 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 45 HIS 0.001 0.000 HIS H 194 PHE 0.010 0.001 PHE A 32 TYR 0.018 0.001 TYR B 230 ARG 0.002 0.000 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 1368) hydrogen bonds : angle 2.56860 ( 4068) SS BOND : bond 0.00084 ( 36) SS BOND : angle 0.55579 ( 72) covalent geometry : bond 0.00246 (20148) covalent geometry : angle 0.44558 (27288) ********************** 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 519 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 488 time to evaluate : 2.240 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 13 LYS cc_start: 0.9064 (tttt) cc_final: 0.8771 (ttmm) REVERT: A 42 GLU cc_start: 0.8305 (tt0) cc_final: 0.7484 (tm-30) REVERT: A 67 ASP cc_start: 0.8694 (t0) cc_final: 0.8313 (t0) REVERT: G 13 LYS cc_start: 0.8915 (tttt) cc_final: 0.8602 (ttmm) REVERT: G 15 GLN cc_start: 0.8971 (mt0) cc_final: 0.8720 (mt0) REVERT: G 42 GLU cc_start: 0.8531 (tt0) cc_final: 0.7756 (tm-30) REVERT: G 55 ASN cc_start: 0.8912 (t0) cc_final: 0.8566 (t0) REVERT: B 13 LYS cc_start: 0.8859 (tttt) cc_final: 0.8530 (ttmm) REVERT: B 39 THR cc_start: 0.8872 (m) cc_final: 0.8636 (m) REVERT: B 42 GLU cc_start: 0.8315 (tt0) cc_final: 0.7678 (tm-30) REVERT: B 47 ASP cc_start: 0.9103 (p0) cc_final: 0.8849 (p0) REVERT: B 67 ASP cc_start: 0.8920 (t0) cc_final: 0.8704 (t0) REVERT: B 101 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7711 (mtp-110) REVERT: B 153 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7888 (mtm180) REVERT: C 13 LYS cc_start: 0.8893 (tttt) cc_final: 0.8579 (ttmm) REVERT: C 42 GLU cc_start: 0.8496 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 47 ASP cc_start: 0.9079 (p0) cc_final: 0.8821 (p0) REVERT: C 55 ASN cc_start: 0.8926 (t0) cc_final: 0.8613 (t0) REVERT: C 104 GLU cc_start: 0.8931 (tt0) cc_final: 0.8712 (tp30) REVERT: D 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8654 (ttmm) REVERT: D 42 GLU cc_start: 0.8271 (tt0) cc_final: 0.7491 (tm-30) REVERT: D 67 ASP cc_start: 0.8703 (t0) cc_final: 0.8310 (t0) REVERT: D 106 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5865 (mp) REVERT: D 227 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8333 (mm-30) REVERT: E 13 LYS cc_start: 0.8817 (tttt) cc_final: 0.8455 (ttmm) REVERT: E 39 THR cc_start: 0.8759 (m) cc_final: 0.8515 (m) REVERT: E 42 GLU cc_start: 0.8348 (tt0) cc_final: 0.7800 (tm-30) REVERT: E 47 ASP cc_start: 0.9104 (p0) cc_final: 0.8869 (p0) REVERT: E 101 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7667 (mtp-110) REVERT: E 227 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8062 (mm-30) REVERT: F 13 LYS cc_start: 0.8921 (tttt) cc_final: 0.8646 (ttmm) REVERT: F 42 GLU cc_start: 0.8425 (tt0) cc_final: 0.7770 (tm-30) REVERT: F 55 ASN cc_start: 0.8940 (t0) cc_final: 0.8578 (t0) REVERT: H 13 LYS cc_start: 0.8990 (tttt) cc_final: 0.8629 (ttmm) REVERT: H 42 GLU cc_start: 0.8346 (tt0) cc_final: 0.7494 (tm-30) REVERT: H 106 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.6031 (mp) REVERT: H 109 LYS cc_start: 0.4736 (OUTLIER) cc_final: 0.4521 (tttm) REVERT: I 13 LYS cc_start: 0.8808 (tttt) cc_final: 0.8447 (ttmm) REVERT: I 42 GLU cc_start: 0.8350 (tt0) cc_final: 0.7682 (tm-30) REVERT: I 101 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7614 (mtp-110) REVERT: J 13 LYS cc_start: 0.8897 (tttt) cc_final: 0.8609 (ttmm) REVERT: J 42 GLU cc_start: 0.8396 (tt0) cc_final: 0.7754 (tm-30) REVERT: J 55 ASN cc_start: 0.8908 (t0) cc_final: 0.8541 (t0) REVERT: K 13 LYS cc_start: 0.8996 (tttt) cc_final: 0.8664 (ttmm) REVERT: K 42 GLU cc_start: 0.8358 (tt0) cc_final: 0.7513 (tm-30) REVERT: K 67 ASP cc_start: 0.8742 (t0) cc_final: 0.8540 (t0) REVERT: L 13 LYS cc_start: 0.8806 (tttt) cc_final: 0.8450 (ttmm) REVERT: L 35 LEU cc_start: 0.8677 (tp) cc_final: 0.8376 (tt) REVERT: L 39 THR cc_start: 0.8808 (m) cc_final: 0.8536 (m) REVERT: L 42 GLU cc_start: 0.8384 (tt0) cc_final: 0.7835 (tm-30) REVERT: L 47 ASP cc_start: 0.9107 (p0) cc_final: 0.8867 (p0) REVERT: L 101 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7743 (mtp-110) REVERT: L 189 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7831 (ttt180) REVERT: L 227 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7990 (mm-30) outliers start: 31 outliers final: 27 residues processed: 500 average time/residue: 0.3510 time to fit residues: 256.3199 Evaluate side-chains 514 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 484 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 171 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 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 212 PHE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 109 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN D 55 ASN H 55 ASN K 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098629 restraints weight = 28985.338| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.54 r_work: 0.3065 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20184 Z= 0.115 Angle : 0.450 5.477 27360 Z= 0.243 Chirality : 0.034 0.163 3096 Planarity : 0.003 0.028 3300 Dihedral : 2.997 12.766 2592 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.62 % Allowed : 18.56 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.17), residues: 2364 helix: 3.39 (0.12), residues: 1680 sheet: 2.31 (0.47), residues: 132 loop : -1.82 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE A 32 TYR 0.022 0.001 TYR J 230 ARG 0.002 0.000 ARG K 101 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1368) hydrogen bonds : angle 2.58753 ( 4068) SS BOND : bond 0.00088 ( 36) SS BOND : angle 0.55678 ( 72) covalent geometry : bond 0.00261 (20148) covalent geometry : angle 0.44921 (27288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8503.09 seconds wall clock time: 146 minutes 34.18 seconds (8794.18 seconds total)