Starting phenix.real_space_refine on Sat Aug 23 01:01:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce5_16599/08_2025/8ce5_16599.map" } resolution = 3.62 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= 0.001 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 5847 2.51 5 N 1550 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1587 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 491 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 8979 At special positions: 0 Unit cell: (102.726, 75.508, 108.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 2 11.99 O 1532 8.00 N 1550 7.00 C 5847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 206.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 67.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.274A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.889A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.990A pdb=" N ASP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.115A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 removed outlier: 3.780A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.572A pdb=" N ARG B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.930A pdb=" N GLN B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 119 removed outlier: 4.522A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.773A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 185 removed outlier: 4.438A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix removed outlier: 3.572A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 3.804A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 42 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 55 through 82 removed outlier: 3.881A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 4.553A pdb=" N ILE C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 115 removed outlier: 4.166A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 128 through 149 removed outlier: 3.822A pdb=" N PHE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 183 Proline residue: C 171 - end of helix removed outlier: 3.646A pdb=" N GLU C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 229 removed outlier: 3.688A pdb=" N GLU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.902A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 13 Processing helix chain 'D' and resid 17 through 63 removed outlier: 3.582A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.699A pdb=" N SER D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 4.365A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 116 removed outlier: 3.503A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 140 removed outlier: 3.628A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 144 Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.732A pdb=" N GLN a 177 " --> pdb=" O GLN a 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 15 Processing helix chain 'b' and resid 21 through 40 removed outlier: 4.233A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE b 28 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 42 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 66 through 77 removed outlier: 4.456A pdb=" N PHE b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP b 72 " --> pdb=" O ARG b 68 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP b 73 " --> pdb=" O LEU b 69 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 4.318A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 4.426A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix Processing helix chain 'b' and resid 122 through 153 Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix removed outlier: 4.271A pdb=" N GLY b 153 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 162 Processing helix chain 'b' and resid 166 through 168 No H-bonds generated for 'chain 'b' and resid 166 through 168' Processing helix chain 'b' and resid 169 through 185 removed outlier: 4.005A pdb=" N MET b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 219 removed outlier: 3.652A pdb=" N ILE b 195 " --> pdb=" O GLY b 191 " (cutoff:3.500A) Proline residue: b 208 - end of helix removed outlier: 3.641A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE b 219 " --> pdb=" O LEU b 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 5.570A pdb=" N ALA A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 61 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU A 8 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU A 59 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'a' and resid 17 through 26 removed outlier: 6.901A pdb=" N LEU a 18 " --> pdb=" O GLU a 12 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU a 12 " --> pdb=" O LEU a 18 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER a 20 " --> pdb=" O LEU a 10 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU a 10 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU a 22 " --> pdb=" O GLU a 8 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU a 4 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 31 through 34 removed outlier: 3.819A pdb=" N ILE a 199 " --> pdb=" O GLN a 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.214A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1512 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: 0.97 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 9 1.22 - 1.37: 2973 1.37 - 1.52: 3175 1.52 - 1.67: 2960 1.67 - 1.82: 79 Bond restraints: 9196 Sorted by residual: bond pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta sigma weight residual 1.453 1.333 0.121 1.22e-02 6.72e+03 9.77e+01 bond pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 1.503 1.196 0.307 3.40e-02 8.65e+02 8.14e+01 bond pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " ideal model delta sigma weight residual 1.492 1.070 0.422 5.00e-02 4.00e+02 7.12e+01 bond pdb=" C4 ATP A 303 " pdb=" C5 ATP A 303 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.74: 12554 14.74 - 29.49: 3 29.49 - 44.23: 3 44.23 - 58.97: 0 58.97 - 73.72: 1 Bond angle restraints: 12561 Sorted by residual: angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 109.91 29.96 1.00e+00 1.00e+00 8.97e+02 angle pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 106.10 179.82 -73.72 3.20e+00 9.77e-02 5.31e+02 angle pdb=" PB ATP A 303 " pdb=" O3B ATP A 303 " pdb=" PG ATP A 303 " ideal model delta sigma weight residual 139.87 117.97 21.90 1.00e+00 1.00e+00 4.80e+02 angle pdb=" PA ATP A 302 " pdb=" O3A ATP A 302 " pdb=" PB ATP A 302 " ideal model delta sigma weight residual 136.83 115.48 21.35 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PA ATP A 303 " pdb=" O3A ATP A 303 " pdb=" PB ATP A 303 " ideal model delta sigma weight residual 136.83 115.64 21.19 1.00e+00 1.00e+00 4.49e+02 ... (remaining 12556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4566 17.71 - 35.42: 630 35.42 - 53.13: 176 53.13 - 70.84: 33 70.84 - 88.55: 19 Dihedral angle restraints: 5424 sinusoidal: 2154 harmonic: 3270 Sorted by residual: dihedral pdb=" CA LEU A 78 " pdb=" C LEU A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA HIS C 60 " pdb=" C HIS C 60 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA VAL C 76 " pdb=" C VAL C 76 " pdb=" N ALA C 77 " pdb=" CA ALA C 77 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1449 0.125 - 0.250: 31 0.250 - 0.374: 1 0.374 - 0.499: 0 0.499 - 0.624: 2 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CG LEU b 108 " pdb=" CB LEU b 108 " pdb=" CD1 LEU b 108 " pdb=" CD2 LEU b 108 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" CB ILE A 124 " pdb=" CA ILE A 124 " pdb=" CG1 ILE A 124 " pdb=" CG2 ILE A 124 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CB THR b 169 " pdb=" CA THR b 169 " pdb=" OG1 THR b 169 " pdb=" CG2 THR b 169 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1480 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " 0.104 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO B 113 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 166 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO b 167 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO b 167 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO b 167 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU b 42 " -0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO b 43 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO b 43 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO b 43 " -0.045 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 104 2.64 - 3.20: 7763 3.20 - 3.77: 14527 3.77 - 4.33: 18434 4.33 - 4.90: 30581 Nonbonded interactions: 71409 Sorted by model distance: nonbonded pdb=" OG1 THR a 43 " pdb="MG MG a 301 " model vdw 2.072 2.170 nonbonded pdb="MG MG A 301 " pdb=" O3G ATP A 302 " model vdw 2.203 2.170 nonbonded pdb=" OG1 THR A 43 " pdb="MG MG A 301 " model vdw 2.228 2.170 nonbonded pdb=" OG1 THR A 92 " pdb=" OE1 GLU A 95 " model vdw 2.254 3.040 nonbonded pdb=" NH1 ARG a 16 " pdb=" O GLY a 39 " model vdw 2.263 3.120 ... (remaining 71404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 301) selection = (chain 'a' and resid 2 through 301) } ncs_group { reference = chain 'B' selection = chain 'b' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.080 Find NCS groups from input model: 0.090 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: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.008 0.422 9196 Z= 0.406 Angle : 1.417 73.718 12561 Z= 0.803 Chirality : 0.054 0.624 1483 Planarity : 0.010 0.146 1547 Dihedral : 18.252 88.553 3310 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 0.32 % Allowed : 27.45 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.24), residues: 1134 helix: -0.42 (0.18), residues: 715 sheet: -2.41 (0.75), residues: 45 loop : -1.94 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.034 0.002 TYR C 58 PHE 0.036 0.002 PHE b 28 TRP 0.027 0.002 TRP C 122 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00845 ( 9196) covalent geometry : angle 1.41735 (12561) hydrogen bonds : bond 0.12961 ( 509) hydrogen bonds : angle 6.09337 ( 1512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 TRP cc_start: 0.7688 (t60) cc_final: 0.7372 (t60) REVERT: a 195 LYS cc_start: 0.7429 (ptpp) cc_final: 0.6883 (tppt) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.0794 time to fit residues: 16.1334 Evaluate side-chains 141 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 7 GLN C 49 GLN C 52 ASN C 169 ASN a 101 HIS a 127 ASN b 23 ASN b 81 GLN b 220 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.209661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.179347 restraints weight = 10422.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179482 restraints weight = 9319.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181172 restraints weight = 8235.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.181547 restraints weight = 7154.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181907 restraints weight = 6680.709| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9196 Z= 0.157 Angle : 0.675 9.622 12561 Z= 0.334 Chirality : 0.042 0.278 1483 Planarity : 0.007 0.085 1547 Dihedral : 10.583 86.657 1299 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 3.77 % Allowed : 24.54 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.25), residues: 1134 helix: 0.40 (0.19), residues: 722 sheet: -2.66 (0.69), residues: 50 loop : -1.73 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 135 TYR 0.008 0.001 TYR A 100 PHE 0.012 0.001 PHE b 28 TRP 0.013 0.001 TRP C 66 HIS 0.003 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9196) covalent geometry : angle 0.67475 (12561) hydrogen bonds : bond 0.03995 ( 509) hydrogen bonds : angle 4.78710 ( 1512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.236 Fit side-chains REVERT: A 91 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8473 (mt) REVERT: B 85 LEU cc_start: 0.7349 (mt) cc_final: 0.6985 (mt) REVERT: a 156 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: a 195 LYS cc_start: 0.7608 (ptpp) cc_final: 0.7289 (tppt) outliers start: 35 outliers final: 16 residues processed: 176 average time/residue: 0.0760 time to fit residues: 18.5087 Evaluate side-chains 162 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 83 HIS a 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.207750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177664 restraints weight = 10488.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.177578 restraints weight = 10307.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178996 restraints weight = 9261.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179329 restraints weight = 7780.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181618 restraints weight = 7267.610| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9196 Z= 0.149 Angle : 0.646 7.291 12561 Z= 0.317 Chirality : 0.042 0.226 1483 Planarity : 0.006 0.077 1547 Dihedral : 9.587 80.748 1296 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 4.52 % Allowed : 24.33 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 1134 helix: 0.76 (0.20), residues: 724 sheet: -2.56 (0.70), residues: 50 loop : -1.57 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 135 TYR 0.015 0.001 TYR B 192 PHE 0.013 0.001 PHE A 99 TRP 0.013 0.001 TRP C 180 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9196) covalent geometry : angle 0.64581 (12561) hydrogen bonds : bond 0.03862 ( 509) hydrogen bonds : angle 4.64008 ( 1512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.271 Fit side-chains REVERT: B 2 MET cc_start: 0.6751 (tpp) cc_final: 0.6455 (tpp) REVERT: C 58 TYR cc_start: 0.6629 (m-80) cc_final: 0.6417 (m-80) REVERT: C 179 TRP cc_start: 0.7851 (t60) cc_final: 0.7126 (t60) REVERT: a 84 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7215 (mm-40) REVERT: a 195 LYS cc_start: 0.7628 (ptpp) cc_final: 0.7404 (tppt) REVERT: b 42 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6307 (mt-10) REVERT: b 101 TRP cc_start: 0.7362 (t60) cc_final: 0.7097 (t60) outliers start: 42 outliers final: 30 residues processed: 186 average time/residue: 0.0808 time to fit residues: 20.6721 Evaluate side-chains 180 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 42 GLU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.202325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171565 restraints weight = 10565.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.171982 restraints weight = 9563.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.173818 restraints weight = 8218.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174024 restraints weight = 7143.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174492 restraints weight = 6781.898| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9196 Z= 0.153 Angle : 0.639 7.130 12561 Z= 0.316 Chirality : 0.042 0.188 1483 Planarity : 0.006 0.070 1547 Dihedral : 9.463 81.463 1296 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 5.17 % Allowed : 25.30 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.25), residues: 1134 helix: 0.92 (0.20), residues: 731 sheet: -2.40 (0.73), residues: 50 loop : -1.42 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.024 0.001 TYR B 192 PHE 0.019 0.001 PHE A 24 TRP 0.011 0.001 TRP C 66 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9196) covalent geometry : angle 0.63856 (12561) hydrogen bonds : bond 0.03762 ( 509) hydrogen bonds : angle 4.58424 ( 1512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.274 Fit side-chains REVERT: a 84 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7199 (mm-40) REVERT: a 195 LYS cc_start: 0.7730 (ptpp) cc_final: 0.7428 (tppt) REVERT: b 42 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: b 101 TRP cc_start: 0.7416 (t60) cc_final: 0.7143 (t60) outliers start: 48 outliers final: 34 residues processed: 189 average time/residue: 0.0801 time to fit residues: 20.9147 Evaluate side-chains 184 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 42 GLU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 127 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.203516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174130 restraints weight = 10438.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173607 restraints weight = 10275.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175358 restraints weight = 9307.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175637 restraints weight = 7861.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176045 restraints weight = 7205.631| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9196 Z= 0.138 Angle : 0.631 9.762 12561 Z= 0.310 Chirality : 0.041 0.315 1483 Planarity : 0.006 0.066 1547 Dihedral : 9.334 81.342 1296 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 4.95 % Allowed : 26.26 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.26), residues: 1134 helix: 1.07 (0.20), residues: 729 sheet: -2.37 (0.72), residues: 50 loop : -1.41 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 136 TYR 0.020 0.001 TYR B 192 PHE 0.022 0.001 PHE A 24 TRP 0.012 0.001 TRP A 80 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9196) covalent geometry : angle 0.63130 (12561) hydrogen bonds : bond 0.03541 ( 509) hydrogen bonds : angle 4.48453 ( 1512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.320 Fit side-chains REVERT: a 84 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7208 (mm-40) REVERT: a 193 GLU cc_start: 0.7646 (tp30) cc_final: 0.7412 (tp30) REVERT: a 195 LYS cc_start: 0.7720 (ptpp) cc_final: 0.7369 (tppt) REVERT: b 101 TRP cc_start: 0.7412 (t60) cc_final: 0.7123 (t60) outliers start: 46 outliers final: 30 residues processed: 185 average time/residue: 0.0747 time to fit residues: 19.8026 Evaluate side-chains 178 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164197 restraints weight = 10784.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163965 restraints weight = 11752.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165271 restraints weight = 11425.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165564 restraints weight = 9408.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166023 restraints weight = 8354.395| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 9196 Z= 0.293 Angle : 0.808 9.732 12561 Z= 0.392 Chirality : 0.048 0.393 1483 Planarity : 0.006 0.065 1547 Dihedral : 9.442 80.625 1296 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 6.57 % Allowed : 25.30 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.25), residues: 1134 helix: 0.59 (0.19), residues: 733 sheet: -2.45 (0.74), residues: 50 loop : -1.47 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 136 TYR 0.013 0.002 TYR B 192 PHE 0.022 0.002 PHE a 156 TRP 0.018 0.002 TRP C 66 HIS 0.008 0.002 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00741 ( 9196) covalent geometry : angle 0.80818 (12561) hydrogen bonds : bond 0.04715 ( 509) hydrogen bonds : angle 4.85034 ( 1512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 0.214 Fit side-chains REVERT: A 24 PHE cc_start: 0.8485 (p90) cc_final: 0.8270 (p90) REVERT: C 59 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (mp) REVERT: C 80 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8061 (tp) REVERT: C 221 MET cc_start: 0.7780 (tpt) cc_final: 0.7396 (ttt) REVERT: a 49 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7817 (mp) REVERT: a 156 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.6431 (m-10) REVERT: a 193 GLU cc_start: 0.7585 (tp30) cc_final: 0.7366 (tp30) REVERT: a 195 LYS cc_start: 0.7796 (ptpp) cc_final: 0.7563 (tppt) REVERT: b 101 TRP cc_start: 0.7682 (t60) cc_final: 0.7480 (t60) outliers start: 61 outliers final: 41 residues processed: 191 average time/residue: 0.0800 time to fit residues: 21.1724 Evaluate side-chains 185 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.198566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168016 restraints weight = 10639.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167958 restraints weight = 11111.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169332 restraints weight = 9819.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170221 restraints weight = 8116.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170519 restraints weight = 7257.745| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9196 Z= 0.145 Angle : 0.672 8.728 12561 Z= 0.328 Chirality : 0.042 0.251 1483 Planarity : 0.006 0.062 1547 Dihedral : 9.339 80.678 1296 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 4.74 % Allowed : 27.99 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1134 helix: 0.94 (0.20), residues: 734 sheet: -2.33 (0.75), residues: 50 loop : -1.45 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 136 TYR 0.012 0.001 TYR B 192 PHE 0.022 0.001 PHE A 24 TRP 0.011 0.001 TRP B 101 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9196) covalent geometry : angle 0.67176 (12561) hydrogen bonds : bond 0.03794 ( 509) hydrogen bonds : angle 4.57128 ( 1512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.217 Fit side-chains REVERT: A 24 PHE cc_start: 0.8468 (p90) cc_final: 0.8255 (p90) REVERT: C 221 MET cc_start: 0.7741 (tpt) cc_final: 0.7302 (ttt) REVERT: b 101 TRP cc_start: 0.7555 (t60) cc_final: 0.7310 (t60) outliers start: 44 outliers final: 27 residues processed: 173 average time/residue: 0.0772 time to fit residues: 18.7240 Evaluate side-chains 166 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.197919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167694 restraints weight = 10492.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167208 restraints weight = 10233.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168756 restraints weight = 9372.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169652 restraints weight = 7958.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169954 restraints weight = 7079.474| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9196 Z= 0.167 Angle : 0.687 8.235 12561 Z= 0.334 Chirality : 0.043 0.262 1483 Planarity : 0.006 0.061 1547 Dihedral : 9.189 79.184 1296 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 4.84 % Allowed : 27.99 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1134 helix: 0.93 (0.20), residues: 733 sheet: -2.26 (0.76), residues: 50 loop : -1.34 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 136 TYR 0.012 0.001 TYR B 192 PHE 0.019 0.001 PHE A 24 TRP 0.012 0.001 TRP b 126 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9196) covalent geometry : angle 0.68655 (12561) hydrogen bonds : bond 0.03885 ( 509) hydrogen bonds : angle 4.59969 ( 1512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.200 Fit side-chains REVERT: B 85 LEU cc_start: 0.7476 (mt) cc_final: 0.7048 (mt) REVERT: C 221 MET cc_start: 0.7735 (tpt) cc_final: 0.7272 (ttt) REVERT: a 16 ARG cc_start: 0.5793 (ttm170) cc_final: 0.4852 (ttp-110) REVERT: a 195 LYS cc_start: 0.7791 (ptpp) cc_final: 0.7075 (tppt) REVERT: b 101 TRP cc_start: 0.7555 (t60) cc_final: 0.7283 (t60) outliers start: 45 outliers final: 35 residues processed: 171 average time/residue: 0.0788 time to fit residues: 18.9724 Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 82 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.203489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.172473 restraints weight = 10389.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173792 restraints weight = 10637.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174752 restraints weight = 9139.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.175231 restraints weight = 7800.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.175513 restraints weight = 7165.249| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9196 Z= 0.128 Angle : 0.647 11.506 12561 Z= 0.313 Chirality : 0.041 0.200 1483 Planarity : 0.006 0.060 1547 Dihedral : 9.025 80.544 1296 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 3.44 % Allowed : 29.17 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.26), residues: 1134 helix: 1.13 (0.20), residues: 733 sheet: -2.15 (0.76), residues: 50 loop : -1.28 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.010 0.001 TYR a 100 PHE 0.020 0.001 PHE A 24 TRP 0.013 0.001 TRP C 179 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9196) covalent geometry : angle 0.64721 (12561) hydrogen bonds : bond 0.03413 ( 509) hydrogen bonds : angle 4.44620 ( 1512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.266 Fit side-chains REVERT: B 85 LEU cc_start: 0.7404 (mt) cc_final: 0.6956 (mt) REVERT: B 180 MET cc_start: 0.7619 (ttm) cc_final: 0.7180 (mtp) REVERT: C 219 MET cc_start: 0.6115 (ttp) cc_final: 0.5910 (ttt) REVERT: C 221 MET cc_start: 0.7724 (tpt) cc_final: 0.7261 (ttt) REVERT: a 16 ARG cc_start: 0.5863 (ttm170) cc_final: 0.4982 (ttp-110) REVERT: a 49 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7860 (mp) REVERT: a 80 TRP cc_start: 0.8566 (t-100) cc_final: 0.7876 (t-100) REVERT: a 195 LYS cc_start: 0.7725 (ptpp) cc_final: 0.7080 (tppt) REVERT: b 101 TRP cc_start: 0.7527 (t60) cc_final: 0.7232 (t60) outliers start: 32 outliers final: 26 residues processed: 165 average time/residue: 0.0814 time to fit residues: 18.6885 Evaluate side-chains 167 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166431 restraints weight = 10559.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166742 restraints weight = 10112.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168188 restraints weight = 9052.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169812 restraints weight = 7816.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170056 restraints weight = 7016.252| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9196 Z= 0.198 Angle : 0.716 7.884 12561 Z= 0.348 Chirality : 0.045 0.278 1483 Planarity : 0.006 0.059 1547 Dihedral : 8.926 75.983 1296 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 3.77 % Allowed : 29.17 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1134 helix: 0.89 (0.19), residues: 735 sheet: -2.35 (0.73), residues: 50 loop : -1.26 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 136 TYR 0.026 0.002 TYR C 58 PHE 0.017 0.002 PHE A 24 TRP 0.017 0.002 TRP C 66 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 9196) covalent geometry : angle 0.71596 (12561) hydrogen bonds : bond 0.04092 ( 509) hydrogen bonds : angle 4.58601 ( 1512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.258 Fit side-chains REVERT: C 221 MET cc_start: 0.7726 (tpt) cc_final: 0.7268 (ttt) REVERT: a 16 ARG cc_start: 0.6068 (ttm170) cc_final: 0.5158 (ttp-110) REVERT: a 49 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7771 (mp) REVERT: a 195 LYS cc_start: 0.7835 (ptpp) cc_final: 0.7013 (tppt) REVERT: b 101 TRP cc_start: 0.7618 (t60) cc_final: 0.7334 (t60) outliers start: 35 outliers final: 33 residues processed: 164 average time/residue: 0.0804 time to fit residues: 18.7491 Evaluate side-chains 175 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 53 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 127 ASN a 186 HIS a 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.202213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.171852 restraints weight = 10364.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172698 restraints weight = 9251.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173346 restraints weight = 8074.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.173776 restraints weight = 7538.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.174347 restraints weight = 7025.326| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.131 Angle : 0.653 7.812 12561 Z= 0.317 Chirality : 0.041 0.213 1483 Planarity : 0.006 0.058 1547 Dihedral : 8.916 80.990 1296 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 29.60 % Favored : 66.95 % 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 aren not related in a simple way. whole: 0.34 (0.26), residues: 1134 helix: 1.11 (0.20), residues: 739 sheet: -2.25 (0.72), residues: 50 loop : -1.25 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 216 TYR 0.017 0.001 TYR C 58 PHE 0.019 0.001 PHE A 24 TRP 0.014 0.001 TRP b 126 HIS 0.002 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9196) covalent geometry : angle 0.65349 (12561) hydrogen bonds : bond 0.03468 ( 509) hydrogen bonds : angle 4.41593 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.77 seconds wall clock time: 19 minutes 58.62 seconds (1198.62 seconds total)