Starting phenix.real_space_refine on Thu Jul 2 13:37:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_16599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_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_16599/07_2026/8ce5_16599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_16599.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_16599.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_16599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_16599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce5_16599/07_2026/8ce5_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-dev-6108/lib/python3.11/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: 1.83, per 1000 atoms: 0.20 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: 0.47 Conformation dependent library (CDL) restraints added in 445.2 milliseconds 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: 0.12 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: 1.20 Time building geometry restraints manager: 0.67 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 - 17.58: 4544 17.58 - 35.16: 607 35.16 - 52.73: 173 52.73 - 70.31: 28 70.31 - 87.89: 10 Dihedral angle restraints: 5362 sinusoidal: 2092 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 5359 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: 1.000 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.280 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 17.397 87.890 3248 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 are 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/Z covalent geometry : bond 0.00845 / 0.41 ( 9196) covalent geometry : angle 1.41735 / 0.80 (12561) hydrogen bonds : bond 0.12961 / 8.45 ( 509) hydrogen bonds : angle 6.09337 / 4.23 ( 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 : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 TRP cc_start: 0.7689 (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: 0.0912 time to fit residues: 18.8077 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 : 0.325 ------------------------------------------------------------------------------- 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... A 154 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.209642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179075 restraints weight = 10425.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.178666 restraints weight = 10482.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.180448 restraints weight = 9700.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181250 restraints weight = 7829.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181538 restraints weight = 7157.263| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9196 Z= 0.152 Angle : 0.675 9.654 12561 Z= 0.333 Chirality : 0.042 0.281 1483 Planarity : 0.007 0.085 1547 Dihedral : 5.286 44.054 1237 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 4.20 % Allowed : 24.33 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.25), residues: 1134 helix: 0.41 (0.19), residues: 722 sheet: -2.67 (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 0.009 0.001 TYR a 100 PHE 0.014 0.001 PHE b 28 TRP 0.014 0.001 TRP C 66 HIS 0.002 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 9196) covalent geometry : angle 0.67451 / 0.33 (12561) hydrogen bonds : bond 0.03989 / 2.73 ( 509) hydrogen bonds : angle 4.78753 / 3.27 ( 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 191 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.315 Fit side-chains REVERT: A 91 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (mt) REVERT: B 85 LEU cc_start: 0.7386 (mt) cc_final: 0.7023 (mt) REVERT: C 58 TYR cc_start: 0.6475 (m-80) cc_final: 0.6158 (m-80) REVERT: a 156 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: a 195 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7322 (tppt) outliers start: 39 outliers final: 17 residues processed: 179 average time/residue: 0.0813 time to fit residues: 20.6035 Evaluate side-chains 161 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 23 SER 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: 0.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN a 83 HIS ** a 127 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 = 0.4370 r_free = 0.4370 target = 0.207310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178458 restraints weight = 10498.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178188 restraints weight = 10462.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180035 restraints weight = 9473.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180711 restraints weight = 7459.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180934 restraints weight = 6905.719| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1669 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= 0.152 Angle : 0.647 7.231 12561 Z= 0.318 Chirality : 0.042 0.230 1483 Planarity : 0.006 0.078 1547 Dihedral : 4.837 31.843 1234 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 4.52 % Allowed : 24.22 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1134 helix: 0.76 (0.20), residues: 719 sheet: -2.54 (0.70), residues: 50 loop : -1.62 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 135 TYR 0.011 0.001 TYR B 192 PHE 0.014 0.001 PHE A 99 TRP 0.012 0.001 TRP C 180 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 9196) covalent geometry : angle 0.64737 / 0.32 (12561) hydrogen bonds : bond 0.03888 / 2.65 ( 509) hydrogen bonds : angle 4.64441 / 3.15 ( 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 198 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.310 Fit side-chains REVERT: B 2 MET cc_start: 0.6798 (tpp) cc_final: 0.6506 (tpp) REVERT: C 179 TRP cc_start: 0.7874 (t60) cc_final: 0.7148 (t60) REVERT: a 84 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7243 (mm-40) REVERT: b 42 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: b 101 TRP cc_start: 0.7403 (t60) cc_final: 0.7135 (t60) outliers start: 42 outliers final: 30 residues processed: 187 average time/residue: 0.0826 time to fit residues: 21.1017 Evaluate side-chains 178 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 93 VAL 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 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: 4.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN a 127 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 = 0.4318 r_free = 0.4318 target = 0.200887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169966 restraints weight = 10613.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170635 restraints weight = 10895.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171696 restraints weight = 9463.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172009 restraints weight = 8289.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174114 restraints weight = 7578.757| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9196 Z= 0.166 Angle : 0.652 7.020 12561 Z= 0.322 Chirality : 0.042 0.198 1483 Planarity : 0.006 0.070 1547 Dihedral : 4.818 31.437 1234 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 5.17 % Allowed : 25.08 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1134 helix: 0.89 (0.20), residues: 730 sheet: -2.41 (0.73), residues: 50 loop : -1.43 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 135 TYR 0.023 0.002 TYR B 192 PHE 0.019 0.002 PHE b 35 TRP 0.013 0.001 TRP A 80 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 9196) covalent geometry : angle 0.65230 / 0.32 (12561) hydrogen bonds : bond 0.03872 / 2.63 ( 509) hydrogen bonds : angle 4.62291 / 3.14 ( 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 203 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.309 Fit side-chains REVERT: C 58 TYR cc_start: 0.6934 (m-80) cc_final: 0.6712 (m-80) REVERT: b 42 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6361 (mt-10) REVERT: b 101 TRP cc_start: 0.7542 (t60) cc_final: 0.7272 (t60) outliers start: 48 outliers final: 32 residues processed: 187 average time/residue: 0.0916 time to fit residues: 24.1302 Evaluate side-chains 181 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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 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 a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 171 MET 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 170 ILE 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: 1.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.199189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169591 restraints weight = 10517.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170703 restraints weight = 10385.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172465 restraints weight = 9048.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172986 restraints weight = 6849.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173806 restraints weight = 6295.736| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9196 Z= 0.171 Angle : 0.671 10.209 12561 Z= 0.327 Chirality : 0.043 0.340 1483 Planarity : 0.006 0.065 1547 Dihedral : 4.796 30.031 1234 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 6.57 % Allowed : 25.73 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1134 helix: 0.93 (0.20), residues: 729 sheet: -2.34 (0.73), residues: 50 loop : -1.46 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 136 TYR 0.008 0.001 TYR B 192 PHE 0.013 0.001 PHE b 28 TRP 0.021 0.001 TRP A 80 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 ( 9196) covalent geometry : angle 0.67054 / 0.33 (12561) hydrogen bonds : bond 0.03844 / 2.62 ( 509) hydrogen bonds : angle 4.61868 / 3.13 ( 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 214 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.305 Fit side-chains REVERT: B 2 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6667 (tpp) REVERT: C 221 MET cc_start: 0.7742 (tpt) cc_final: 0.7331 (ttt) REVERT: a 49 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7923 (mp) REVERT: a 193 GLU cc_start: 0.7648 (tp30) cc_final: 0.7446 (tp30) REVERT: b 101 TRP cc_start: 0.7508 (t60) cc_final: 0.7253 (t60) outliers start: 61 outliers final: 40 residues processed: 197 average time/residue: 0.0882 time to fit residues: 24.7691 Evaluate side-chains 182 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 2 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 TRP 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 131 LEU Chi-restraints excluded: chain B residue 133 LEU 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 140 VAL 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 a residue 5 GLU Chi-restraints excluded: chain a residue 49 LEU 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 56 VAL 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: 5.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 0.0270 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.195020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163154 restraints weight = 10663.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.163397 restraints weight = 10633.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164632 restraints weight = 9430.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165166 restraints weight = 8409.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165925 restraints weight = 7648.665| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9196 Z= 0.210 Angle : 0.732 9.111 12561 Z= 0.356 Chirality : 0.045 0.349 1483 Planarity : 0.006 0.064 1547 Dihedral : 4.943 32.114 1234 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 7.43 % Allowed : 25.30 % 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 are not related in a simple way. whole: -0.05 (0.25), residues: 1134 helix: 0.80 (0.20), residues: 727 sheet: -2.28 (0.73), residues: 50 loop : -1.33 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 136 TYR 0.010 0.002 TYR A 100 PHE 0.030 0.002 PHE A 24 TRP 0.018 0.002 TRP A 80 HIS 0.005 0.001 HIS a 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.21 ( 9196) covalent geometry : angle 0.73245 / 0.36 (12561) hydrogen bonds : bond 0.04217 / 2.86 ( 509) hydrogen bonds : angle 4.73080 / 3.20 ( 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 212 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 143 time to evaluate : 0.353 Fit side-chains REVERT: C 80 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 221 MET cc_start: 0.7759 (tpt) cc_final: 0.7337 (ttt) REVERT: a 156 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: b 101 TRP cc_start: 0.7619 (t60) cc_final: 0.7353 (t60) outliers start: 69 outliers final: 47 residues processed: 189 average time/residue: 0.0839 time to fit residues: 22.7518 Evaluate side-chains 189 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 111 GLU 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 64 LEU 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 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 80 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL 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 215 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 38 HIS 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 189 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 109 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 127 ASN 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 = 0.4320 r_free = 0.4320 target = 0.201095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.171378 restraints weight = 10559.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171193 restraints weight = 10760.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172347 restraints weight = 9721.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173202 restraints weight = 8091.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.173637 restraints weight = 7294.469| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9196 Z= 0.137 Angle : 0.656 8.837 12561 Z= 0.321 Chirality : 0.041 0.225 1483 Planarity : 0.006 0.061 1547 Dihedral : 4.717 30.417 1234 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 4.63 % Allowed : 28.09 % 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 are not related in a simple way. whole: 0.24 (0.26), residues: 1134 helix: 1.08 (0.20), residues: 733 sheet: -2.14 (0.73), residues: 50 loop : -1.40 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 152 TYR 0.013 0.001 TYR B 192 PHE 0.028 0.001 PHE A 24 TRP 0.019 0.001 TRP A 80 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9196) covalent geometry : angle 0.65633 / 0.32 (12561) hydrogen bonds : bond 0.03552 / 2.43 ( 509) hydrogen bonds : angle 4.48939 / 3.04 ( 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 189 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.333 Fit side-chains REVERT: C 198 MET cc_start: 0.6252 (tpt) cc_final: 0.5981 (tpt) REVERT: C 221 MET cc_start: 0.7790 (tpt) cc_final: 0.7297 (ttt) REVERT: a 16 ARG cc_start: 0.5703 (ttm170) cc_final: 0.4797 (ttp-110) REVERT: a 49 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7867 (mp) REVERT: b 101 TRP cc_start: 0.7497 (t60) cc_final: 0.7219 (t60) outliers start: 43 outliers final: 27 residues processed: 175 average time/residue: 0.0951 time to fit residues: 23.4478 Evaluate side-chains 167 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 95 GLU 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 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 43 PHE Chi-restraints excluded: chain C residue 74 MET 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 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 ASN ** 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 = 0.4268 r_free = 0.4268 target = 0.195118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164612 restraints weight = 10580.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164908 restraints weight = 10168.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165850 restraints weight = 8930.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166632 restraints weight = 7885.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.166874 restraints weight = 7319.395| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9196 Z= 0.207 Angle : 0.726 7.962 12561 Z= 0.350 Chirality : 0.045 0.287 1483 Planarity : 0.006 0.061 1547 Dihedral : 4.810 30.384 1234 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 4.63 % Allowed : 28.31 % 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 are not related in a simple way. whole: 0.04 (0.25), residues: 1134 helix: 0.87 (0.20), residues: 733 sheet: -2.37 (0.70), residues: 50 loop : -1.31 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 136 TYR 0.010 0.001 TYR A 100 PHE 0.031 0.002 PHE A 24 TRP 0.017 0.002 TRP A 80 HIS 0.004 0.001 HIS a 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 ( 9196) covalent geometry : angle 0.72571 / 0.35 (12561) hydrogen bonds : bond 0.04112 / 2.81 ( 509) hydrogen bonds : angle 4.64695 / 3.14 ( 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 183 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.340 Fit side-chains REVERT: C 221 MET cc_start: 0.7732 (tpt) cc_final: 0.7302 (ttt) REVERT: a 16 ARG cc_start: 0.5900 (ttm170) cc_final: 0.4984 (ttp-110) REVERT: a 49 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7846 (mp) REVERT: b 101 TRP cc_start: 0.7617 (t60) cc_final: 0.7356 (t60) outliers start: 43 outliers final: 31 residues processed: 167 average time/residue: 0.0950 time to fit residues: 22.4024 Evaluate side-chains 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain B residue 129 MET 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 161 ILE 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 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 95 GLU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 196 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 109 optimal weight: 0.0170 chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4209 r_free = 0.4209 target = 0.192931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164001 restraints weight = 9500.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164932 restraints weight = 8329.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166020 restraints weight = 7324.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166561 restraints weight = 6330.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167001 restraints weight = 5932.334| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9196 Z= 0.133 Angle : 0.669 8.682 12561 Z= 0.320 Chirality : 0.041 0.228 1483 Planarity : 0.006 0.059 1547 Dihedral : 4.671 29.562 1234 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 3.66 % Allowed : 28.96 % 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 are not related in a simple way. whole: 0.28 (0.26), residues: 1134 helix: 1.06 (0.20), residues: 742 sheet: -2.20 (0.71), residues: 50 loop : -1.30 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.010 0.001 TYR a 100 PHE 0.036 0.001 PHE A 24 TRP 0.017 0.001 TRP A 80 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 9196) covalent geometry : angle 0.66857 / 0.32 (12561) hydrogen bonds : bond 0.03509 / 2.41 ( 509) hydrogen bonds : angle 4.48908 / 3.04 ( 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 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.278 Fit side-chains REVERT: B 85 LEU cc_start: 0.7368 (mt) cc_final: 0.6908 (mt) REVERT: C 221 MET cc_start: 0.7752 (tpt) cc_final: 0.7295 (ttt) REVERT: a 16 ARG cc_start: 0.5942 (ttm170) cc_final: 0.5098 (ttp-110) REVERT: a 49 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7872 (mp) REVERT: a 80 TRP cc_start: 0.8587 (t-100) cc_final: 0.7670 (t60) REVERT: b 101 TRP cc_start: 0.7534 (t60) cc_final: 0.7238 (t60) outliers start: 34 outliers final: 27 residues processed: 159 average time/residue: 0.0930 time to fit residues: 20.8059 Evaluate side-chains 164 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 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 43 PHE 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 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 49 LEU 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 196 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 HIS 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 = 0.4208 r_free = 0.4208 target = 0.192816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.163652 restraints weight = 9493.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164649 restraints weight = 8331.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.165430 restraints weight = 7367.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165992 restraints weight = 6505.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166451 restraints weight = 6084.908| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3037 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= 0.140 Angle : 0.671 9.066 12561 Z= 0.322 Chirality : 0.042 0.224 1483 Planarity : 0.006 0.060 1547 Dihedral : 4.630 27.602 1234 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 3.34 % Allowed : 29.28 % 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 are not related in a simple way. whole: 0.31 (0.26), residues: 1134 helix: 1.09 (0.20), residues: 742 sheet: -2.22 (0.70), residues: 50 loop : -1.30 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 146 TYR 0.012 0.001 TYR C 58 PHE 0.034 0.001 PHE A 24 TRP 0.016 0.001 TRP A 80 HIS 0.002 0.001 HIS a 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9196) covalent geometry : angle 0.67112 / 0.32 (12561) hydrogen bonds : bond 0.03533 / 2.42 ( 509) hydrogen bonds : angle 4.46262 / 3.03 ( 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 167 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.321 Fit side-chains REVERT: B 85 LEU cc_start: 0.7386 (mt) cc_final: 0.6950 (mt) REVERT: C 221 MET cc_start: 0.7726 (tpt) cc_final: 0.7286 (ttt) REVERT: a 3 MET cc_start: 0.6585 (mmt) cc_final: 0.6030 (ptt) REVERT: a 16 ARG cc_start: 0.5952 (ttm170) cc_final: 0.5083 (ttp-110) REVERT: a 80 TRP cc_start: 0.8563 (t-100) cc_final: 0.8210 (t60) REVERT: b 101 TRP cc_start: 0.7502 (t60) cc_final: 0.7237 (t60) outliers start: 31 outliers final: 28 residues processed: 157 average time/residue: 0.0890 time to fit residues: 19.9200 Evaluate side-chains 163 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 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 43 PHE 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 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.185038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155628 restraints weight = 9618.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157174 restraints weight = 10007.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158978 restraints weight = 7928.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159102 restraints weight = 6529.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.160853 restraints weight = 6048.173| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9196 Z= 0.228 Angle : 0.766 11.402 12561 Z= 0.368 Chirality : 0.046 0.367 1483 Planarity : 0.006 0.061 1547 Dihedral : 4.826 30.115 1234 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.76 % Favored : 95.06 % Rotamer: Outliers : 3.12 % Allowed : 29.28 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1134 helix: 0.79 (0.19), residues: 735 sheet: -2.34 (0.71), residues: 48 loop : -1.30 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 12 TYR 0.025 0.002 TYR C 58 PHE 0.032 0.002 PHE b 28 TRP 0.019 0.002 TRP C 66 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 ( 9196) covalent geometry : angle 0.76584 / 0.37 (12561) hydrogen bonds : bond 0.04367 / 2.96 ( 509) hydrogen bonds : angle 4.72888 / 3.19 ( 1512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.15 seconds wall clock time: 23 minutes 48.64 seconds (1428.64 seconds total)