Starting phenix.real_space_refine on Wed Mar 4 18:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmx_0923/03_2026/6lmx_0923.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 153 5.16 5 C 10062 2.51 5 N 2628 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15588 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1732 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 230} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 5, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 1.74, per 1000 atoms: 0.11 Number of scatterers: 15588 At special positions: 0 Unit cell: (128.65, 128.65, 101.789, 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 153 16.00 O 2745 8.00 N 2628 7.00 C 10062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.01 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.01 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 160 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 691.5 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4122 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 51 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 167 through 200 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.713A pdb=" N PHE B 137 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 167 through 200 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 167 through 200 Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 210 through 248 removed outlier: 3.592A pdb=" N PHE C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE D 137 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 167 through 200 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE E 137 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 167 through 200 Processing helix chain 'E' and resid 203 through 208 Processing helix chain 'E' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR F 51 " --> pdb=" O TYR F 47 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 removed outlier: 3.672A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE F 137 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 167 through 200 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE F 248 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 258 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR G 51 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.721A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 143 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 167 through 200 Processing helix chain 'G' and resid 203 through 208 Processing helix chain 'G' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 258 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR H 50 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 51 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 72 through 83 removed outlier: 3.719A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.540A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 137 removed outlier: 3.713A pdb=" N PHE H 137 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 167 through 200 Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE H 248 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 258 Processing helix chain 'I' and resid 22 through 37 Processing helix chain 'I' and resid 44 through 70 removed outlier: 4.510A pdb=" N TYR I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 72 through 83 removed outlier: 3.720A pdb=" N ARG I 83 " --> pdb=" O GLU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 107 removed outlier: 3.671A pdb=" N TYR I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 121 Processing helix chain 'I' and resid 121 through 129 removed outlier: 3.539A pdb=" N SER I 129 " --> pdb=" O LEU I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 removed outlier: 3.712A pdb=" N PHE I 137 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 143 Processing helix chain 'I' and resid 147 through 156 Processing helix chain 'I' and resid 167 through 200 Processing helix chain 'I' and resid 203 through 208 Processing helix chain 'I' and resid 210 through 248 removed outlier: 3.591A pdb=" N PHE I 248 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 258 1252 hydrogen bonds defined for protein. 3621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2833 1.32 - 1.44: 4009 1.44 - 1.57: 8827 1.57 - 1.69: 0 1.69 - 1.81: 234 Bond restraints: 15903 Sorted by residual: bond pdb=" C CYS I 43 " pdb=" N MET I 44 " ideal model delta sigma weight residual 1.333 1.241 0.091 2.74e-02 1.33e+03 1.11e+01 bond pdb=" C CYS D 43 " pdb=" N MET D 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS H 43 " pdb=" N MET H 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS C 43 " pdb=" N MET C 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 bond pdb=" C CYS B 43 " pdb=" N MET B 44 " ideal model delta sigma weight residual 1.333 1.242 0.091 2.74e-02 1.33e+03 1.10e+01 ... (remaining 15898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 20128 2.41 - 4.82: 1286 4.82 - 7.23: 199 7.23 - 9.64: 14 9.64 - 12.05: 18 Bond angle restraints: 21645 Sorted by residual: angle pdb=" CG1 ILE I 177 " pdb=" CB ILE I 177 " pdb=" CG2 ILE I 177 " ideal model delta sigma weight residual 110.70 98.65 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE D 177 " pdb=" CB ILE D 177 " pdb=" CG2 ILE D 177 " ideal model delta sigma weight residual 110.70 98.67 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE C 177 " pdb=" CB ILE C 177 " pdb=" CG2 ILE C 177 " ideal model delta sigma weight residual 110.70 98.67 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE G 177 " pdb=" CB ILE G 177 " pdb=" CG2 ILE G 177 " ideal model delta sigma weight residual 110.70 98.68 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CG1 ILE A 177 " pdb=" CB ILE A 177 " pdb=" CG2 ILE A 177 " ideal model delta sigma weight residual 110.70 98.68 12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 21640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 8307 16.91 - 33.83: 1043 33.83 - 50.74: 163 50.74 - 67.66: 36 67.66 - 84.57: 9 Dihedral angle restraints: 9558 sinusoidal: 3231 harmonic: 6327 Sorted by residual: dihedral pdb=" CA LYS E 255 " pdb=" C LYS E 255 " pdb=" N ASP E 256 " pdb=" CA ASP E 256 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LYS I 255 " pdb=" C LYS I 255 " pdb=" N ASP I 256 " pdb=" CA ASP I 256 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LYS F 255 " pdb=" C LYS F 255 " pdb=" N ASP F 256 " pdb=" CA ASP F 256 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 9555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1563 0.054 - 0.107: 781 0.107 - 0.161: 153 0.161 - 0.215: 33 0.215 - 0.268: 35 Chirality restraints: 2565 Sorted by residual: chirality pdb=" CB THR B 174 " pdb=" CA THR B 174 " pdb=" OG1 THR B 174 " pdb=" CG2 THR B 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR H 174 " pdb=" CA THR H 174 " pdb=" OG1 THR H 174 " pdb=" CG2 THR H 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB THR F 174 " pdb=" CA THR F 174 " pdb=" OG1 THR F 174 " pdb=" CG2 THR F 174 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2562 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO E 60 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.089 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 60 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 59 " 0.089 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO I 60 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO I 60 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO I 60 " 0.072 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1435 2.71 - 3.26: 14986 3.26 - 3.80: 24087 3.80 - 4.35: 29294 4.35 - 4.90: 51377 Nonbonded interactions: 121179 Sorted by model distance: nonbonded pdb=" O LEU B 118 " pdb=" OG SER B 181 " model vdw 2.161 3.040 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 181 " model vdw 2.161 3.040 nonbonded pdb=" O LEU H 118 " pdb=" OG SER H 181 " model vdw 2.161 3.040 nonbonded pdb=" O LEU D 118 " pdb=" OG SER D 181 " model vdw 2.162 3.040 nonbonded pdb=" O LEU I 118 " pdb=" OG SER I 181 " model vdw 2.162 3.040 ... (remaining 121174 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.390 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.019 0.159 15921 Z= 0.741 Angle : 1.325 12.048 21681 Z= 0.755 Chirality : 0.067 0.268 2565 Planarity : 0.013 0.133 2736 Dihedral : 15.243 84.572 5382 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 12.79 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.20 (0.10), residues: 2142 helix: -4.30 (0.05), residues: 1629 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 175 TYR 0.032 0.005 TYR H 176 PHE 0.047 0.005 PHE I 124 TRP 0.019 0.004 TRP C 113 Details of bonding type rmsd covalent geometry : bond 0.01877 (15903) covalent geometry : angle 1.32085 (21645) SS BOND : bond 0.01424 ( 18) SS BOND : angle 2.99148 ( 36) hydrogen bonds : bond 0.27591 ( 1252) hydrogen bonds : angle 10.38007 ( 3621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 282 time to evaluate : 0.613 Fit side-chains REVERT: A 38 GLU cc_start: 0.8114 (pm20) cc_final: 0.7765 (pm20) REVERT: A 96 ARG cc_start: 0.6860 (ptt180) cc_final: 0.6151 (mtt180) REVERT: A 104 GLN cc_start: 0.8142 (mp10) cc_final: 0.7697 (mp10) REVERT: A 157 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7183 (mtm-85) REVERT: A 168 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: B 46 GLU cc_start: 0.8271 (pm20) cc_final: 0.8044 (pm20) REVERT: B 96 ARG cc_start: 0.6558 (ptt180) cc_final: 0.5889 (mtt180) REVERT: B 104 GLN cc_start: 0.8535 (mp10) cc_final: 0.8184 (mp10) REVERT: B 105 ARG cc_start: 0.6521 (ttt90) cc_final: 0.6297 (ttm-80) REVERT: B 120 ASP cc_start: 0.8939 (t0) cc_final: 0.8699 (t0) REVERT: B 133 ASP cc_start: 0.8628 (t0) cc_final: 0.8020 (t0) REVERT: B 157 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7117 (mtm-85) REVERT: B 167 ASN cc_start: 0.8924 (t0) cc_final: 0.8649 (t0) REVERT: B 168 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: C 38 GLU cc_start: 0.8167 (pm20) cc_final: 0.7916 (pm20) REVERT: C 96 ARG cc_start: 0.6745 (ptt180) cc_final: 0.6052 (mtt180) REVERT: C 104 GLN cc_start: 0.8070 (mp10) cc_final: 0.7232 (mp10) REVERT: C 148 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 165 GLU cc_start: 0.6935 (pm20) cc_final: 0.6702 (pm20) REVERT: C 168 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: D 44 MET cc_start: 0.8809 (mtm) cc_final: 0.8600 (mtm) REVERT: D 96 ARG cc_start: 0.6791 (ptt180) cc_final: 0.5927 (mtt180) REVERT: D 119 MET cc_start: 0.8807 (mmt) cc_final: 0.8521 (mmm) REVERT: D 133 ASP cc_start: 0.8683 (t0) cc_final: 0.8302 (t0) REVERT: D 143 VAL cc_start: 0.8805 (m) cc_final: 0.8452 (t) REVERT: D 146 MET cc_start: 0.6478 (ptp) cc_final: 0.5952 (ptp) REVERT: D 150 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 151 LYS cc_start: 0.7812 (tptt) cc_final: 0.7523 (tptt) REVERT: D 153 LYS cc_start: 0.8754 (mttt) cc_final: 0.8252 (mttp) REVERT: D 161 LYS cc_start: 0.8347 (mttm) cc_final: 0.8141 (tptp) REVERT: D 168 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: E 44 MET cc_start: 0.8663 (mtm) cc_final: 0.8421 (mtt) REVERT: E 96 ARG cc_start: 0.6490 (ptt180) cc_final: 0.5465 (mtt-85) REVERT: E 104 GLN cc_start: 0.8257 (mp10) cc_final: 0.7925 (mp10) REVERT: E 119 MET cc_start: 0.8891 (mmt) cc_final: 0.8501 (mmm) REVERT: E 168 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: F 96 ARG cc_start: 0.6757 (ptt180) cc_final: 0.6175 (mtt180) REVERT: F 104 GLN cc_start: 0.8205 (mp10) cc_final: 0.7870 (mp10) REVERT: F 133 ASP cc_start: 0.8527 (t0) cc_final: 0.8074 (t0) REVERT: F 157 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7621 (mtp85) REVERT: F 168 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: G 96 ARG cc_start: 0.6288 (ptt180) cc_final: 0.5676 (mtt180) REVERT: G 104 GLN cc_start: 0.7943 (mp10) cc_final: 0.7675 (mp10) REVERT: G 119 MET cc_start: 0.8783 (mmt) cc_final: 0.8328 (mmt) REVERT: G 133 ASP cc_start: 0.8633 (t0) cc_final: 0.8288 (t0) REVERT: G 165 GLU cc_start: 0.5887 (pm20) cc_final: 0.5589 (pm20) REVERT: G 168 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: G 191 MET cc_start: 0.7175 (mmt) cc_final: 0.6877 (mmm) REVERT: H 46 GLU cc_start: 0.8306 (pm20) cc_final: 0.8030 (pm20) REVERT: H 82 LYS cc_start: 0.4291 (OUTLIER) cc_final: 0.4014 (tppp) REVERT: H 96 ARG cc_start: 0.6708 (ptt180) cc_final: 0.5921 (mtt180) REVERT: H 133 ASP cc_start: 0.8669 (t0) cc_final: 0.8422 (t0) REVERT: H 143 VAL cc_start: 0.8815 (m) cc_final: 0.8608 (m) REVERT: H 153 LYS cc_start: 0.8661 (mttt) cc_final: 0.8460 (mtmm) REVERT: H 157 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7453 (mtp85) REVERT: H 168 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: I 38 GLU cc_start: 0.8125 (pm20) cc_final: 0.7852 (pm20) REVERT: I 44 MET cc_start: 0.8832 (mtm) cc_final: 0.8500 (mtm) REVERT: I 96 ARG cc_start: 0.6388 (ptt180) cc_final: 0.5704 (mtt180) REVERT: I 104 GLN cc_start: 0.7912 (mp10) cc_final: 0.7583 (mp10) REVERT: I 143 VAL cc_start: 0.8524 (m) cc_final: 0.8241 (t) REVERT: I 168 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6956 (tm-30) outliers start: 18 outliers final: 0 residues processed: 300 average time/residue: 0.1586 time to fit residues: 65.5945 Evaluate side-chains 277 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain I residue 168 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN B 72 ASN C 71 ASN C 72 ASN D 71 ASN D 72 ASN E 71 ASN F 71 ASN F 72 ASN G 71 ASN H 71 ASN H 72 ASN I 71 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.217725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.146176 restraints weight = 16205.211| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.61 r_work: 0.3180 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15921 Z= 0.136 Angle : 0.593 4.713 21681 Z= 0.329 Chirality : 0.037 0.122 2565 Planarity : 0.009 0.082 2736 Dihedral : 6.287 44.690 2326 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.49 % Allowed : 13.42 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.15), residues: 2142 helix: -1.20 (0.10), residues: 1647 sheet: None (None), residues: 0 loop : -1.77 (0.22), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 170 TYR 0.015 0.002 TYR D 34 PHE 0.017 0.001 PHE C 197 TRP 0.015 0.001 TRP D 62 Details of bonding type rmsd covalent geometry : bond 0.00270 (15903) covalent geometry : angle 0.59255 (21645) SS BOND : bond 0.00059 ( 18) SS BOND : angle 0.65402 ( 36) hydrogen bonds : bond 0.04674 ( 1252) hydrogen bonds : angle 4.48925 ( 3621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.8781 (ttm) cc_final: 0.8562 (ttt) REVERT: A 34 TYR cc_start: 0.9033 (t80) cc_final: 0.8802 (t80) REVERT: A 104 GLN cc_start: 0.7989 (mp10) cc_final: 0.7424 (mp10) REVERT: B 33 MET cc_start: 0.8484 (ttm) cc_final: 0.8207 (ttm) REVERT: B 38 GLU cc_start: 0.8532 (pm20) cc_final: 0.8132 (pm20) REVERT: B 46 GLU cc_start: 0.8526 (pm20) cc_final: 0.8224 (pm20) REVERT: B 157 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: C 33 MET cc_start: 0.8721 (ttm) cc_final: 0.8019 (ttt) REVERT: C 34 TYR cc_start: 0.9131 (t80) cc_final: 0.8901 (t80) REVERT: C 104 GLN cc_start: 0.8080 (mp10) cc_final: 0.7555 (mp10) REVERT: C 143 VAL cc_start: 0.8625 (m) cc_final: 0.8243 (t) REVERT: C 161 LYS cc_start: 0.8833 (tptm) cc_final: 0.8503 (tptp) REVERT: C 191 MET cc_start: 0.7756 (mmt) cc_final: 0.7502 (mmm) REVERT: C 198 LEU cc_start: 0.8841 (mt) cc_final: 0.8415 (tt) REVERT: D 38 GLU cc_start: 0.8736 (pm20) cc_final: 0.8528 (pm20) REVERT: D 44 MET cc_start: 0.8805 (mtm) cc_final: 0.8481 (mtm) REVERT: D 143 VAL cc_start: 0.8316 (m) cc_final: 0.7979 (t) REVERT: D 146 MET cc_start: 0.6419 (ptp) cc_final: 0.6213 (ptp) REVERT: D 150 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 151 LYS cc_start: 0.7940 (tptt) cc_final: 0.7712 (tptt) REVERT: D 153 LYS cc_start: 0.8734 (mttt) cc_final: 0.8255 (mttp) REVERT: D 161 LYS cc_start: 0.8575 (mttm) cc_final: 0.8362 (tptp) REVERT: D 198 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8009 (tt) REVERT: E 33 MET cc_start: 0.8533 (ttm) cc_final: 0.7782 (ttm) REVERT: E 104 GLN cc_start: 0.8004 (mp10) cc_final: 0.7578 (mp10) REVERT: E 119 MET cc_start: 0.8862 (mmt) cc_final: 0.8614 (mmp) REVERT: E 136 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8565 (mtpp) REVERT: E 153 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8349 (mtpt) REVERT: E 191 MET cc_start: 0.7784 (mmt) cc_final: 0.7514 (mmm) REVERT: F 33 MET cc_start: 0.8499 (ttm) cc_final: 0.8148 (ttt) REVERT: F 104 GLN cc_start: 0.8301 (mp10) cc_final: 0.7869 (mp10) REVERT: F 119 MET cc_start: 0.8901 (mmt) cc_final: 0.8654 (mmp) REVERT: F 133 ASP cc_start: 0.7952 (t0) cc_final: 0.7666 (t0) REVERT: F 143 VAL cc_start: 0.8734 (m) cc_final: 0.8408 (t) REVERT: F 198 LEU cc_start: 0.8585 (mt) cc_final: 0.8281 (tt) REVERT: G 38 GLU cc_start: 0.8662 (pm20) cc_final: 0.8289 (pm20) REVERT: G 119 MET cc_start: 0.8788 (mmt) cc_final: 0.8560 (mmp) REVERT: G 133 ASP cc_start: 0.8624 (t0) cc_final: 0.8280 (t0) REVERT: G 143 VAL cc_start: 0.8679 (m) cc_final: 0.8035 (t) REVERT: G 191 MET cc_start: 0.7839 (mmt) cc_final: 0.7618 (mmm) REVERT: H 33 MET cc_start: 0.8875 (ttm) cc_final: 0.8659 (ttt) REVERT: H 38 GLU cc_start: 0.8515 (pm20) cc_final: 0.8199 (pm20) REVERT: H 44 MET cc_start: 0.8910 (mtm) cc_final: 0.8419 (mtm) REVERT: H 46 GLU cc_start: 0.8597 (pm20) cc_final: 0.8379 (pm20) REVERT: H 104 GLN cc_start: 0.8393 (mp10) cc_final: 0.8040 (mp10) REVERT: H 157 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7750 (mtp85) REVERT: H 191 MET cc_start: 0.7963 (mmt) cc_final: 0.7755 (mmm) REVERT: I 191 MET cc_start: 0.7841 (mmt) cc_final: 0.7574 (mmm) outliers start: 50 outliers final: 26 residues processed: 295 average time/residue: 0.1280 time to fit residues: 54.3398 Evaluate side-chains 275 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 0.0050 chunk 67 optimal weight: 9.9990 chunk 151 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 71 ASN F 71 ASN G 71 ASN I 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.220242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146930 restraints weight = 16275.914| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.66 r_work: 0.3296 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15921 Z= 0.125 Angle : 0.516 6.855 21681 Z= 0.278 Chirality : 0.037 0.116 2565 Planarity : 0.007 0.071 2736 Dihedral : 4.438 12.913 2295 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.10 % Allowed : 15.79 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2142 helix: 0.74 (0.12), residues: 1647 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 157 TYR 0.013 0.001 TYR I 34 PHE 0.012 0.001 PHE C 197 TRP 0.012 0.001 TRP D 62 Details of bonding type rmsd covalent geometry : bond 0.00273 (15903) covalent geometry : angle 0.51626 (21645) SS BOND : bond 0.00122 ( 18) SS BOND : angle 0.42601 ( 36) hydrogen bonds : bond 0.03953 ( 1252) hydrogen bonds : angle 3.71672 ( 3621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.8883 (ttm) cc_final: 0.8680 (ttt) REVERT: A 153 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8492 (mtmm) REVERT: A 165 GLU cc_start: 0.6716 (pm20) cc_final: 0.6328 (pm20) REVERT: A 191 MET cc_start: 0.8248 (mmp) cc_final: 0.7680 (ttp) REVERT: B 33 MET cc_start: 0.8692 (ttm) cc_final: 0.7995 (ttm) REVERT: B 38 GLU cc_start: 0.8519 (pm20) cc_final: 0.8173 (pm20) REVERT: C 33 MET cc_start: 0.8593 (ttm) cc_final: 0.7873 (ttt) REVERT: C 34 TYR cc_start: 0.9199 (t80) cc_final: 0.8920 (t80) REVERT: C 104 GLN cc_start: 0.8259 (mp10) cc_final: 0.7754 (mp10) REVERT: C 143 VAL cc_start: 0.8716 (m) cc_final: 0.8252 (t) REVERT: C 161 LYS cc_start: 0.8879 (tptm) cc_final: 0.8574 (tptp) REVERT: D 38 GLU cc_start: 0.8688 (pm20) cc_final: 0.8477 (pm20) REVERT: D 44 MET cc_start: 0.8799 (mtm) cc_final: 0.8390 (mtm) REVERT: D 119 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8338 (mmt) REVERT: D 150 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 153 LYS cc_start: 0.8475 (mttt) cc_final: 0.8024 (mttp) REVERT: D 165 GLU cc_start: 0.6894 (pm20) cc_final: 0.6386 (pm20) REVERT: E 33 MET cc_start: 0.8585 (ttm) cc_final: 0.8028 (ttm) REVERT: E 104 GLN cc_start: 0.8554 (mp10) cc_final: 0.8313 (mp10) REVERT: E 129 SER cc_start: 0.8986 (p) cc_final: 0.8604 (t) REVERT: E 136 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8540 (mtpp) REVERT: E 153 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8315 (mtpt) REVERT: E 191 MET cc_start: 0.7790 (mmt) cc_final: 0.7573 (mmm) REVERT: F 104 GLN cc_start: 0.8576 (mp10) cc_final: 0.8372 (mp10) REVERT: G 38 GLU cc_start: 0.8642 (pm20) cc_final: 0.8288 (pm20) REVERT: G 133 ASP cc_start: 0.8602 (t0) cc_final: 0.8250 (t0) REVERT: G 153 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8286 (mttp) REVERT: G 162 ASP cc_start: 0.8892 (p0) cc_final: 0.8575 (p0) REVERT: H 33 MET cc_start: 0.8565 (ttm) cc_final: 0.8362 (ttt) REVERT: H 38 GLU cc_start: 0.8597 (pm20) cc_final: 0.8277 (pm20) REVERT: H 104 GLN cc_start: 0.8730 (mp10) cc_final: 0.8404 (mp10) REVERT: H 165 GLU cc_start: 0.7289 (pm20) cc_final: 0.6851 (pm20) REVERT: I 71 ASN cc_start: 0.7349 (m110) cc_final: 0.7141 (m-40) REVERT: I 129 SER cc_start: 0.8993 (p) cc_final: 0.8673 (t) outliers start: 30 outliers final: 18 residues processed: 283 average time/residue: 0.1358 time to fit residues: 55.2615 Evaluate side-chains 269 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 250 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 213 optimal weight: 50.0000 chunk 176 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 71 ASN F 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.214186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141713 restraints weight = 16252.660| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.27 r_work: 0.3092 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15921 Z= 0.222 Angle : 0.628 9.734 21681 Z= 0.329 Chirality : 0.041 0.131 2565 Planarity : 0.006 0.073 2736 Dihedral : 4.551 13.901 2295 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.91 % Allowed : 16.56 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2142 helix: 0.99 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 200 TYR 0.024 0.002 TYR A 176 PHE 0.015 0.002 PHE H 39 TRP 0.009 0.002 TRP H 186 Details of bonding type rmsd covalent geometry : bond 0.00547 (15903) covalent geometry : angle 0.62672 (21645) SS BOND : bond 0.00127 ( 18) SS BOND : angle 1.03533 ( 36) hydrogen bonds : bond 0.04198 ( 1252) hydrogen bonds : angle 3.86751 ( 3621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8422 (mmp) cc_final: 0.7938 (ttp) REVERT: B 46 GLU cc_start: 0.8588 (pm20) cc_final: 0.8344 (pm20) REVERT: B 143 VAL cc_start: 0.8619 (m) cc_final: 0.8323 (t) REVERT: C 33 MET cc_start: 0.8641 (ttm) cc_final: 0.8198 (ttm) REVERT: C 104 GLN cc_start: 0.8244 (mp10) cc_final: 0.8027 (mp10) REVERT: C 135 GLU cc_start: 0.8126 (mp0) cc_final: 0.7612 (pp20) REVERT: C 143 VAL cc_start: 0.8662 (m) cc_final: 0.8185 (t) REVERT: C 161 LYS cc_start: 0.8898 (tptm) cc_final: 0.8615 (tptp) REVERT: D 33 MET cc_start: 0.8855 (ttm) cc_final: 0.8492 (ttt) REVERT: D 38 GLU cc_start: 0.8591 (pm20) cc_final: 0.8373 (pm20) REVERT: D 44 MET cc_start: 0.8902 (mtm) cc_final: 0.8453 (mtt) REVERT: D 119 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8212 (mmt) REVERT: D 153 LYS cc_start: 0.8765 (mttt) cc_final: 0.8466 (mttp) REVERT: D 165 GLU cc_start: 0.6642 (pm20) cc_final: 0.6121 (pm20) REVERT: E 33 MET cc_start: 0.8567 (ttm) cc_final: 0.8034 (ttm) REVERT: E 119 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8447 (mmm) REVERT: E 136 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8551 (mtpp) REVERT: E 161 LYS cc_start: 0.8745 (tptm) cc_final: 0.8492 (tptp) REVERT: F 104 GLN cc_start: 0.8558 (mp10) cc_final: 0.8349 (mp10) REVERT: F 119 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8556 (mmp) REVERT: F 143 VAL cc_start: 0.8752 (m) cc_final: 0.8491 (t) REVERT: F 191 MET cc_start: 0.8388 (mmp) cc_final: 0.8061 (mmm) REVERT: G 38 GLU cc_start: 0.8633 (pm20) cc_final: 0.8252 (pm20) REVERT: G 133 ASP cc_start: 0.8684 (t0) cc_final: 0.8328 (t0) REVERT: G 143 VAL cc_start: 0.8540 (m) cc_final: 0.8264 (t) REVERT: G 191 MET cc_start: 0.8026 (mmp) cc_final: 0.7411 (mtt) REVERT: H 33 MET cc_start: 0.8594 (ttm) cc_final: 0.8379 (ttt) REVERT: H 44 MET cc_start: 0.8958 (mtm) cc_final: 0.8429 (mtm) REVERT: H 104 GLN cc_start: 0.8787 (mp10) cc_final: 0.8446 (mp10) outliers start: 56 outliers final: 41 residues processed: 299 average time/residue: 0.1308 time to fit residues: 56.8271 Evaluate side-chains 305 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139944 restraints weight = 16324.556| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.38 r_work: 0.3063 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15921 Z= 0.218 Angle : 0.620 9.177 21681 Z= 0.325 Chirality : 0.040 0.125 2565 Planarity : 0.006 0.072 2736 Dihedral : 4.484 14.037 2295 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.47 % Allowed : 17.89 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2142 helix: 1.23 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 200 TYR 0.020 0.002 TYR A 176 PHE 0.014 0.002 PHE H 39 TRP 0.009 0.002 TRP G 62 Details of bonding type rmsd covalent geometry : bond 0.00538 (15903) covalent geometry : angle 0.61943 (21645) SS BOND : bond 0.00125 ( 18) SS BOND : angle 0.97636 ( 36) hydrogen bonds : bond 0.04136 ( 1252) hydrogen bonds : angle 3.85764 ( 3621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8282 (mp10) cc_final: 0.7959 (mp10) REVERT: A 165 GLU cc_start: 0.6748 (pm20) cc_final: 0.5779 (pm20) REVERT: A 191 MET cc_start: 0.8295 (mmp) cc_final: 0.8056 (mmm) REVERT: B 143 VAL cc_start: 0.8621 (m) cc_final: 0.8380 (t) REVERT: B 191 MET cc_start: 0.8154 (mmp) cc_final: 0.7799 (ttp) REVERT: C 104 GLN cc_start: 0.8301 (mp10) cc_final: 0.8067 (mp10) REVERT: C 135 GLU cc_start: 0.8105 (mp0) cc_final: 0.7566 (pp20) REVERT: C 143 VAL cc_start: 0.8748 (m) cc_final: 0.8388 (t) REVERT: C 161 LYS cc_start: 0.8892 (tptm) cc_final: 0.8561 (tptp) REVERT: D 33 MET cc_start: 0.8779 (ttm) cc_final: 0.8431 (ttt) REVERT: D 38 GLU cc_start: 0.8371 (pm20) cc_final: 0.8144 (pm20) REVERT: D 44 MET cc_start: 0.8885 (mtm) cc_final: 0.8463 (mtt) REVERT: D 119 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8237 (mmt) REVERT: D 133 ASP cc_start: 0.8354 (t70) cc_final: 0.8078 (t0) REVERT: D 153 LYS cc_start: 0.8500 (mttt) cc_final: 0.8198 (mttp) REVERT: D 165 GLU cc_start: 0.6475 (pm20) cc_final: 0.5969 (pm20) REVERT: D 198 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7830 (tt) REVERT: E 33 MET cc_start: 0.8523 (ttm) cc_final: 0.7970 (ttm) REVERT: E 119 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: E 161 LYS cc_start: 0.8779 (tptm) cc_final: 0.8538 (tptp) REVERT: F 104 GLN cc_start: 0.8556 (mp10) cc_final: 0.8327 (mp10) REVERT: F 119 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8502 (mmp) REVERT: F 143 VAL cc_start: 0.8742 (m) cc_final: 0.8222 (t) REVERT: F 151 LYS cc_start: 0.7949 (tptt) cc_final: 0.7718 (tptt) REVERT: F 191 MET cc_start: 0.8215 (mmp) cc_final: 0.7204 (mtm) REVERT: G 104 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: G 133 ASP cc_start: 0.8746 (t0) cc_final: 0.8348 (t0) REVERT: G 191 MET cc_start: 0.7694 (mmp) cc_final: 0.7234 (mtm) REVERT: H 44 MET cc_start: 0.8787 (mtm) cc_final: 0.8244 (mtm) outliers start: 64 outliers final: 48 residues processed: 294 average time/residue: 0.1278 time to fit residues: 55.1763 Evaluate side-chains 307 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 19 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 174 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.219056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170320 restraints weight = 16162.656| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.81 r_work: 0.3223 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15921 Z= 0.121 Angle : 0.516 5.527 21681 Z= 0.271 Chirality : 0.037 0.108 2565 Planarity : 0.006 0.066 2736 Dihedral : 4.108 13.442 2295 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.70 % Allowed : 19.29 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.18), residues: 2142 helix: 1.74 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -1.46 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 157 TYR 0.014 0.001 TYR A 176 PHE 0.009 0.001 PHE C 197 TRP 0.011 0.001 TRP E 62 Details of bonding type rmsd covalent geometry : bond 0.00269 (15903) covalent geometry : angle 0.51572 (21645) SS BOND : bond 0.00149 ( 18) SS BOND : angle 0.56080 ( 36) hydrogen bonds : bond 0.03632 ( 1252) hydrogen bonds : angle 3.50902 ( 3621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8269 (mp10) cc_final: 0.7935 (mp10) REVERT: A 165 GLU cc_start: 0.6669 (pm20) cc_final: 0.5657 (pm20) REVERT: A 191 MET cc_start: 0.7699 (mmp) cc_final: 0.7283 (mtt) REVERT: B 38 GLU cc_start: 0.8194 (pm20) cc_final: 0.7968 (pm20) REVERT: B 157 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7595 (mtm-85) REVERT: B 191 MET cc_start: 0.8061 (mmp) cc_final: 0.7800 (mmm) REVERT: C 34 TYR cc_start: 0.9253 (t80) cc_final: 0.8506 (t80) REVERT: C 104 GLN cc_start: 0.8484 (mp10) cc_final: 0.7526 (mp10) REVERT: C 135 GLU cc_start: 0.7878 (mp0) cc_final: 0.7502 (pp20) REVERT: C 161 LYS cc_start: 0.8782 (tptm) cc_final: 0.8480 (tptp) REVERT: D 44 MET cc_start: 0.8690 (mtm) cc_final: 0.8324 (mtm) REVERT: D 104 GLN cc_start: 0.8381 (mp10) cc_final: 0.8069 (mp10) REVERT: D 119 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8336 (mmt) REVERT: D 153 LYS cc_start: 0.8545 (mttt) cc_final: 0.8234 (mttp) REVERT: D 165 GLU cc_start: 0.6519 (pm20) cc_final: 0.6006 (pm20) REVERT: E 33 MET cc_start: 0.8478 (ttm) cc_final: 0.7802 (ttm) REVERT: E 104 GLN cc_start: 0.8402 (mp10) cc_final: 0.8053 (mp10) REVERT: E 119 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8631 (mmp) REVERT: E 161 LYS cc_start: 0.8683 (tptm) cc_final: 0.8423 (tptm) REVERT: F 104 GLN cc_start: 0.8707 (mp10) cc_final: 0.8487 (mp10) REVERT: F 119 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (mmt) REVERT: F 191 MET cc_start: 0.8049 (mmp) cc_final: 0.7273 (mtp) REVERT: G 38 GLU cc_start: 0.8427 (pm20) cc_final: 0.8086 (pm20) REVERT: G 104 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: G 133 ASP cc_start: 0.8699 (t0) cc_final: 0.8350 (t0) REVERT: G 152 LEU cc_start: 0.8770 (mt) cc_final: 0.8522 (mt) REVERT: G 191 MET cc_start: 0.7442 (mmp) cc_final: 0.7216 (mtt) REVERT: H 38 GLU cc_start: 0.8243 (pm20) cc_final: 0.8026 (pm20) REVERT: H 104 GLN cc_start: 0.8636 (mp10) cc_final: 0.8190 (mp10) REVERT: I 104 GLN cc_start: 0.8518 (mp10) cc_final: 0.7793 (mp10) REVERT: I 129 SER cc_start: 0.8942 (p) cc_final: 0.8635 (t) outliers start: 53 outliers final: 45 residues processed: 303 average time/residue: 0.1324 time to fit residues: 58.5741 Evaluate side-chains 313 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN H 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.204540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154754 restraints weight = 16067.943| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.19 r_work: 0.3159 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15921 Z= 0.123 Angle : 0.513 6.459 21681 Z= 0.269 Chirality : 0.037 0.156 2565 Planarity : 0.005 0.066 2736 Dihedral : 3.973 13.519 2295 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.84 % Allowed : 19.43 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.18), residues: 2142 helix: 1.92 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.27 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 157 TYR 0.013 0.001 TYR A 176 PHE 0.009 0.001 PHE C 197 TRP 0.009 0.001 TRP I 62 Details of bonding type rmsd covalent geometry : bond 0.00279 (15903) covalent geometry : angle 0.51305 (21645) SS BOND : bond 0.00108 ( 18) SS BOND : angle 0.58672 ( 36) hydrogen bonds : bond 0.03491 ( 1252) hydrogen bonds : angle 3.42865 ( 3621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 0.607 Fit side-chains REVERT: A 104 GLN cc_start: 0.8254 (mp10) cc_final: 0.7446 (mp10) REVERT: A 165 GLU cc_start: 0.6582 (pm20) cc_final: 0.5608 (pm20) REVERT: A 191 MET cc_start: 0.8136 (mmp) cc_final: 0.7625 (mtt) REVERT: B 38 GLU cc_start: 0.8285 (pm20) cc_final: 0.8044 (pm20) REVERT: B 157 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7648 (mtm-85) REVERT: C 104 GLN cc_start: 0.8644 (mp10) cc_final: 0.7688 (mp10) REVERT: C 135 GLU cc_start: 0.7985 (mp0) cc_final: 0.7543 (pp20) REVERT: C 143 VAL cc_start: 0.8752 (m) cc_final: 0.8231 (t) REVERT: C 151 LYS cc_start: 0.7544 (tptt) cc_final: 0.7226 (tptt) REVERT: C 161 LYS cc_start: 0.8860 (tptm) cc_final: 0.8504 (tptp) REVERT: D 44 MET cc_start: 0.8754 (mtm) cc_final: 0.8304 (mtt) REVERT: D 104 GLN cc_start: 0.8517 (mp10) cc_final: 0.8171 (mp10) REVERT: D 119 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8389 (mmt) REVERT: D 153 LYS cc_start: 0.8513 (mttt) cc_final: 0.8208 (mttp) REVERT: D 165 GLU cc_start: 0.6571 (pm20) cc_final: 0.6035 (pm20) REVERT: E 104 GLN cc_start: 0.8531 (mp10) cc_final: 0.8163 (mp10) REVERT: E 119 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8721 (mmt) REVERT: E 153 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8364 (mtpt) REVERT: E 161 LYS cc_start: 0.8865 (tptm) cc_final: 0.8656 (tptp) REVERT: F 104 GLN cc_start: 0.8640 (mp10) cc_final: 0.8433 (mp10) REVERT: F 119 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8703 (mmt) REVERT: F 161 LYS cc_start: 0.8559 (tptp) cc_final: 0.8353 (tptp) REVERT: F 191 MET cc_start: 0.8218 (mmp) cc_final: 0.7353 (mtp) REVERT: G 38 GLU cc_start: 0.8553 (pm20) cc_final: 0.8204 (pm20) REVERT: G 104 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: G 133 ASP cc_start: 0.8669 (t0) cc_final: 0.8353 (t0) REVERT: G 143 VAL cc_start: 0.8182 (t) cc_final: 0.7787 (m) REVERT: G 191 MET cc_start: 0.7686 (mmp) cc_final: 0.7315 (mtt) REVERT: H 38 GLU cc_start: 0.8333 (pm20) cc_final: 0.8084 (pm20) REVERT: H 104 GLN cc_start: 0.8656 (mp10) cc_final: 0.8093 (mp10) REVERT: I 104 GLN cc_start: 0.8579 (mp10) cc_final: 0.7892 (mp10) REVERT: I 129 SER cc_start: 0.8929 (p) cc_final: 0.8667 (t) outliers start: 55 outliers final: 43 residues processed: 300 average time/residue: 0.1298 time to fit residues: 56.7995 Evaluate side-chains 314 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 203 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN D 71 ASN F 71 ASN H 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.220150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173832 restraints weight = 16103.312| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.67 r_work: 0.3209 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15921 Z= 0.178 Angle : 0.576 8.495 21681 Z= 0.301 Chirality : 0.039 0.120 2565 Planarity : 0.006 0.067 2736 Dihedral : 4.112 14.090 2295 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.68 % Allowed : 19.64 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 2142 helix: 1.84 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.19 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 200 TYR 0.022 0.002 TYR A 176 PHE 0.011 0.001 PHE H 39 TRP 0.008 0.001 TRP F 186 Details of bonding type rmsd covalent geometry : bond 0.00438 (15903) covalent geometry : angle 0.57535 (21645) SS BOND : bond 0.00063 ( 18) SS BOND : angle 0.95164 ( 36) hydrogen bonds : bond 0.03709 ( 1252) hydrogen bonds : angle 3.58014 ( 3621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: A 191 MET cc_start: 0.8427 (mmp) cc_final: 0.7776 (mtt) REVERT: B 38 GLU cc_start: 0.8402 (pm20) cc_final: 0.8158 (pm20) REVERT: B 104 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: B 157 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7732 (mtm-85) REVERT: B 191 MET cc_start: 0.8510 (mmp) cc_final: 0.8235 (mmm) REVERT: C 104 GLN cc_start: 0.8662 (mp10) cc_final: 0.7702 (mp10) REVERT: C 135 GLU cc_start: 0.7998 (mp0) cc_final: 0.7486 (pp20) REVERT: C 161 LYS cc_start: 0.8865 (tptm) cc_final: 0.8506 (tptp) REVERT: D 44 MET cc_start: 0.8894 (mtm) cc_final: 0.8493 (mtm) REVERT: D 119 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8507 (mmt) REVERT: D 153 LYS cc_start: 0.8559 (mttt) cc_final: 0.8253 (mttp) REVERT: D 165 GLU cc_start: 0.6600 (pm20) cc_final: 0.6067 (pm20) REVERT: E 104 GLN cc_start: 0.8490 (mp10) cc_final: 0.8112 (mp10) REVERT: E 119 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8414 (mmm) REVERT: E 153 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8350 (mtpt) REVERT: E 161 LYS cc_start: 0.8905 (tptm) cc_final: 0.8700 (tptp) REVERT: F 104 GLN cc_start: 0.8650 (mp10) cc_final: 0.8428 (mp10) REVERT: F 119 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8469 (mmp) REVERT: F 191 MET cc_start: 0.8431 (mmp) cc_final: 0.7497 (mtp) REVERT: G 104 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: G 133 ASP cc_start: 0.8773 (t0) cc_final: 0.8383 (t0) REVERT: G 191 MET cc_start: 0.7928 (mmp) cc_final: 0.7432 (mtt) REVERT: H 38 GLU cc_start: 0.8540 (pm20) cc_final: 0.8318 (pm20) REVERT: H 104 GLN cc_start: 0.8623 (mp10) cc_final: 0.7998 (mp10) REVERT: I 38 GLU cc_start: 0.8445 (pm20) cc_final: 0.8084 (pm20) REVERT: I 104 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: I 129 SER cc_start: 0.9047 (p) cc_final: 0.8745 (t) outliers start: 67 outliers final: 49 residues processed: 299 average time/residue: 0.1249 time to fit residues: 54.5435 Evaluate side-chains 316 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Chi-restraints excluded: chain I residue 180 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.221323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.166539 restraints weight = 16112.519| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.14 r_work: 0.3137 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15921 Z= 0.125 Angle : 0.521 5.495 21681 Z= 0.274 Chirality : 0.037 0.109 2565 Planarity : 0.005 0.065 2736 Dihedral : 3.957 13.477 2295 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.98 % Allowed : 20.34 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 2142 helix: 2.05 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 157 TYR 0.021 0.001 TYR A 176 PHE 0.008 0.001 PHE C 197 TRP 0.011 0.001 TRP E 62 Details of bonding type rmsd covalent geometry : bond 0.00290 (15903) covalent geometry : angle 0.52151 (21645) SS BOND : bond 0.00045 ( 18) SS BOND : angle 0.51066 ( 36) hydrogen bonds : bond 0.03458 ( 1252) hydrogen bonds : angle 3.43516 ( 3621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: A 165 GLU cc_start: 0.6652 (pm20) cc_final: 0.5600 (pm20) REVERT: B 38 GLU cc_start: 0.8335 (pm20) cc_final: 0.8116 (pm20) REVERT: B 104 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 157 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7683 (mtm-85) REVERT: B 191 MET cc_start: 0.8472 (mmp) cc_final: 0.8247 (mmm) REVERT: C 104 GLN cc_start: 0.8599 (mp10) cc_final: 0.7705 (mp10) REVERT: C 135 GLU cc_start: 0.7961 (mp0) cc_final: 0.7498 (pp20) REVERT: C 143 VAL cc_start: 0.8645 (m) cc_final: 0.8428 (t) REVERT: C 161 LYS cc_start: 0.8880 (tptm) cc_final: 0.8532 (tptp) REVERT: D 104 GLN cc_start: 0.8382 (mp10) cc_final: 0.7755 (mp10) REVERT: D 119 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8349 (mmt) REVERT: D 153 LYS cc_start: 0.8527 (mttt) cc_final: 0.8258 (mttp) REVERT: D 165 GLU cc_start: 0.6722 (pm20) cc_final: 0.6113 (pm20) REVERT: E 33 MET cc_start: 0.8429 (ttm) cc_final: 0.7779 (ttm) REVERT: E 104 GLN cc_start: 0.8566 (mp10) cc_final: 0.8183 (mp10) REVERT: E 153 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8344 (mtpt) REVERT: E 161 LYS cc_start: 0.8889 (tptm) cc_final: 0.8596 (tptm) REVERT: F 104 GLN cc_start: 0.8600 (mp10) cc_final: 0.8395 (mp10) REVERT: F 119 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8617 (mmt) REVERT: F 191 MET cc_start: 0.8301 (mmp) cc_final: 0.7412 (mtp) REVERT: G 33 MET cc_start: 0.8603 (ttm) cc_final: 0.8386 (ttm) REVERT: G 38 GLU cc_start: 0.8539 (pm20) cc_final: 0.8198 (pm20) REVERT: G 104 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: G 133 ASP cc_start: 0.8677 (t0) cc_final: 0.8362 (t0) REVERT: G 191 MET cc_start: 0.7807 (mmp) cc_final: 0.7382 (mtt) REVERT: H 38 GLU cc_start: 0.8421 (pm20) cc_final: 0.8210 (pm20) REVERT: H 104 GLN cc_start: 0.8592 (mp10) cc_final: 0.7956 (mp10) REVERT: I 38 GLU cc_start: 0.8283 (pm20) cc_final: 0.7974 (pm20) REVERT: I 104 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: I 129 SER cc_start: 0.8945 (p) cc_final: 0.8678 (t) outliers start: 57 outliers final: 46 residues processed: 294 average time/residue: 0.1293 time to fit residues: 55.5483 Evaluate side-chains 315 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 16 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN H 71 ASN I 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.212555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165450 restraints weight = 16288.299| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.16 r_work: 0.3087 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15921 Z= 0.251 Angle : 0.665 9.923 21681 Z= 0.345 Chirality : 0.041 0.133 2565 Planarity : 0.006 0.069 2736 Dihedral : 4.303 15.127 2295 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.40 % Allowed : 20.55 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.18), residues: 2142 helix: 1.71 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.12 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 175 TYR 0.032 0.003 TYR A 176 PHE 0.013 0.002 PHE H 64 TRP 0.012 0.002 TRP I 186 Details of bonding type rmsd covalent geometry : bond 0.00624 (15903) covalent geometry : angle 0.66333 (21645) SS BOND : bond 0.00099 ( 18) SS BOND : angle 1.34267 ( 36) hydrogen bonds : bond 0.04004 ( 1252) hydrogen bonds : angle 3.78539 ( 3621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: A 191 MET cc_start: 0.8316 (mmm) cc_final: 0.7827 (mtt) REVERT: B 104 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: B 191 MET cc_start: 0.8381 (mmp) cc_final: 0.8088 (mmm) REVERT: C 104 GLN cc_start: 0.8611 (mp10) cc_final: 0.7667 (mp10) REVERT: C 161 LYS cc_start: 0.8830 (tptm) cc_final: 0.8507 (tptp) REVERT: D 44 MET cc_start: 0.8892 (mtm) cc_final: 0.8543 (mtm) REVERT: D 104 GLN cc_start: 0.8443 (mp10) cc_final: 0.8060 (mp10) REVERT: D 119 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8578 (mmt) REVERT: D 153 LYS cc_start: 0.8576 (mttt) cc_final: 0.8312 (mttp) REVERT: D 165 GLU cc_start: 0.6695 (pm20) cc_final: 0.6095 (pm20) REVERT: E 104 GLN cc_start: 0.8605 (mp10) cc_final: 0.8171 (mp10) REVERT: E 161 LYS cc_start: 0.8899 (tptm) cc_final: 0.8683 (tptp) REVERT: F 104 GLN cc_start: 0.8643 (mp10) cc_final: 0.8413 (mp10) REVERT: F 119 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8569 (mmp) REVERT: F 191 MET cc_start: 0.8364 (mmp) cc_final: 0.8114 (mmm) REVERT: G 104 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: G 133 ASP cc_start: 0.8765 (t0) cc_final: 0.8419 (t0) REVERT: G 191 MET cc_start: 0.7880 (mmp) cc_final: 0.7549 (mtt) REVERT: H 38 GLU cc_start: 0.8333 (pm20) cc_final: 0.8112 (pm20) REVERT: H 44 MET cc_start: 0.8777 (mtm) cc_final: 0.8262 (mtm) REVERT: H 104 GLN cc_start: 0.8634 (mp10) cc_final: 0.7889 (mp10) REVERT: I 38 GLU cc_start: 0.8325 (pm20) cc_final: 0.8015 (pm20) REVERT: I 104 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7851 (mp10) outliers start: 63 outliers final: 50 residues processed: 288 average time/residue: 0.1310 time to fit residues: 55.5418 Evaluate side-chains 302 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 179 CYS Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 179 CYS Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 179 CYS Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 30.0000 chunk 196 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 93 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.220926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165948 restraints weight = 16139.538| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.09 r_work: 0.3147 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15921 Z= 0.129 Angle : 0.550 7.757 21681 Z= 0.287 Chirality : 0.037 0.109 2565 Planarity : 0.005 0.065 2736 Dihedral : 4.047 14.081 2295 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.91 % Allowed : 21.03 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.18), residues: 2142 helix: 2.05 (0.13), residues: 1665 sheet: None (None), residues: 0 loop : -1.00 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 170 TYR 0.020 0.001 TYR A 176 PHE 0.009 0.001 PHE C 197 TRP 0.010 0.001 TRP E 62 Details of bonding type rmsd covalent geometry : bond 0.00302 (15903) covalent geometry : angle 0.55035 (21645) SS BOND : bond 0.00052 ( 18) SS BOND : angle 0.55499 ( 36) hydrogen bonds : bond 0.03527 ( 1252) hydrogen bonds : angle 3.53054 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.97 seconds wall clock time: 62 minutes 20.13 seconds (3740.13 seconds total)