Starting phenix.real_space_refine on Thu Mar 13 11:55:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce5_16599/03_2025/8ce5_16599.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.42, per 1000 atoms: 0.60 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: 3.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.32 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 9 1.22 - 1.37: 2973 1.37 - 1.52: 3175 1.52 - 1.67: 2960 1.67 - 1.82: 79 Bond restraints: 9196 Sorted by residual: bond pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta sigma weight residual 1.453 1.333 0.121 1.22e-02 6.72e+03 9.77e+01 bond pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 1.503 1.196 0.307 3.40e-02 8.65e+02 8.14e+01 bond pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " ideal model delta sigma weight residual 1.492 1.070 0.422 5.00e-02 4.00e+02 7.12e+01 bond pdb=" C4 ATP A 303 " pdb=" C5 ATP A 303 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.74: 12554 14.74 - 29.49: 3 29.49 - 44.23: 3 44.23 - 58.97: 0 58.97 - 73.72: 1 Bond angle restraints: 12561 Sorted by residual: angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 109.91 29.96 1.00e+00 1.00e+00 8.97e+02 angle pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 106.10 179.82 -73.72 3.20e+00 9.77e-02 5.31e+02 angle pdb=" PB ATP A 303 " pdb=" O3B ATP A 303 " pdb=" PG ATP A 303 " ideal model delta sigma weight residual 139.87 117.97 21.90 1.00e+00 1.00e+00 4.80e+02 angle pdb=" PA ATP A 302 " pdb=" O3A ATP A 302 " pdb=" PB ATP A 302 " ideal model delta sigma weight residual 136.83 115.48 21.35 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PA ATP A 303 " pdb=" O3A ATP A 303 " pdb=" PB ATP A 303 " ideal model delta sigma weight residual 136.83 115.64 21.19 1.00e+00 1.00e+00 4.49e+02 ... (remaining 12556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4566 17.71 - 35.42: 630 35.42 - 53.13: 176 53.13 - 70.84: 33 70.84 - 88.55: 19 Dihedral angle restraints: 5424 sinusoidal: 2154 harmonic: 3270 Sorted by residual: dihedral pdb=" CA LEU A 78 " pdb=" C LEU A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA HIS C 60 " pdb=" C HIS C 60 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA VAL C 76 " pdb=" C VAL C 76 " pdb=" N ALA C 77 " pdb=" CA ALA C 77 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1449 0.125 - 0.250: 31 0.250 - 0.374: 1 0.374 - 0.499: 0 0.499 - 0.624: 2 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CG LEU b 108 " pdb=" CB LEU b 108 " pdb=" CD1 LEU b 108 " pdb=" CD2 LEU b 108 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" CB ILE A 124 " pdb=" CA ILE A 124 " pdb=" CG1 ILE A 124 " pdb=" CG2 ILE A 124 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CB THR b 169 " pdb=" CA THR b 169 " pdb=" OG1 THR b 169 " pdb=" CG2 THR b 169 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1480 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " 0.104 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO B 113 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 166 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO b 167 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO b 167 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO b 167 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU b 42 " -0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO b 43 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO b 43 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO b 43 " -0.045 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 104 2.64 - 3.20: 7763 3.20 - 3.77: 14527 3.77 - 4.33: 18434 4.33 - 4.90: 30581 Nonbonded interactions: 71409 Sorted by model distance: nonbonded pdb=" OG1 THR a 43 " pdb="MG MG a 301 " model vdw 2.072 2.170 nonbonded pdb="MG MG A 301 " pdb=" O3G ATP A 302 " model vdw 2.203 2.170 nonbonded pdb=" OG1 THR A 43 " pdb="MG MG A 301 " model vdw 2.228 2.170 nonbonded pdb=" OG1 THR A 92 " pdb=" OE1 GLU A 95 " model vdw 2.254 3.040 nonbonded pdb=" NH1 ARG a 16 " pdb=" O GLY a 39 " model vdw 2.263 3.120 ... (remaining 71404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 203 or resid 301)) selection = (chain 'a' and (resid 2 through 203 or resid 301)) } ncs_group { reference = chain 'B' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.320 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.422 9196 Z= 0.609 Angle : 1.417 73.718 12561 Z= 0.803 Chirality : 0.054 0.624 1483 Planarity : 0.010 0.146 1547 Dihedral : 18.252 88.553 3310 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (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 TRP 0.027 0.002 TRP C 122 HIS 0.007 0.001 HIS A 83 PHE 0.036 0.002 PHE b 28 TYR 0.034 0.002 TYR C 58 ARG 0.008 0.001 ARG B 68 *********************** 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 : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 TRP cc_start: 0.7688 (t60) cc_final: 0.7372 (t60) REVERT: a 195 LYS cc_start: 0.7429 (ptpp) cc_final: 0.6883 (tppt) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.2225 time to fit residues: 45.2640 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 : 0.920 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 7 GLN C 49 GLN C 52 ASN C 169 ASN a 101 HIS a 127 ASN b 23 ASN b 81 GLN b 220 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.211680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181838 restraints weight = 10391.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.182262 restraints weight = 9344.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183638 restraints weight = 8130.449| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1128 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= 0.225 Angle : 0.675 10.071 12561 Z= 0.334 Chirality : 0.042 0.268 1483 Planarity : 0.007 0.087 1547 Dihedral : 10.586 86.851 1299 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 3.77 % Allowed : 24.43 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1134 helix: 0.39 (0.19), residues: 722 sheet: -2.62 (0.69), residues: 50 loop : -1.75 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 66 HIS 0.002 0.001 HIS A 83 PHE 0.013 0.001 PHE b 28 TYR 0.009 0.001 TYR a 100 ARG 0.003 0.000 ARG a 135 *********************** 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 187 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.931 Fit side-chains REVERT: A 91 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 85 LEU cc_start: 0.7319 (mt) cc_final: 0.6928 (mt) REVERT: a 156 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: a 195 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7320 (tppt) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 0.2135 time to fit residues: 51.9769 Evaluate side-chains 161 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 83 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.207360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177462 restraints weight = 10487.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178091 restraints weight = 10678.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180669 restraints weight = 8963.673| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9196 Z= 0.248 Angle : 0.656 7.914 12561 Z= 0.321 Chirality : 0.042 0.234 1483 Planarity : 0.006 0.077 1547 Dihedral : 9.608 80.530 1296 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 4.41 % Allowed : 24.22 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1134 helix: 0.75 (0.20), residues: 718 sheet: -2.62 (0.70), residues: 50 loop : -1.64 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 180 HIS 0.003 0.001 HIS D 43 PHE 0.013 0.001 PHE A 99 TYR 0.015 0.002 TYR C 58 ARG 0.004 0.000 ARG a 135 *********************** 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 193 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 2 MET cc_start: 0.6919 (tpp) cc_final: 0.6483 (tpp) REVERT: a 84 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7181 (mm-40) REVERT: a 141 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8593 (ttm170) REVERT: a 195 LYS cc_start: 0.7650 (ptpp) cc_final: 0.7413 (tppt) REVERT: b 42 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6316 (mt-10) REVERT: b 101 TRP cc_start: 0.7356 (t60) cc_final: 0.7093 (t60) outliers start: 41 outliers final: 28 residues processed: 182 average time/residue: 0.2144 time to fit residues: 53.7234 Evaluate side-chains 175 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 141 ARG 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 16 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 127 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.200977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168677 restraints weight = 10493.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170090 restraints weight = 10566.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170673 restraints weight = 9504.276| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1960 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= 0.260 Angle : 0.658 7.361 12561 Z= 0.323 Chirality : 0.042 0.214 1483 Planarity : 0.006 0.071 1547 Dihedral : 9.453 81.538 1296 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 5.49 % Allowed : 24.87 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1134 helix: 0.90 (0.20), residues: 730 sheet: -2.32 (0.75), residues: 50 loop : -1.45 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 66 HIS 0.003 0.001 HIS C 184 PHE 0.022 0.002 PHE A 24 TYR 0.010 0.001 TYR C 58 ARG 0.004 0.000 ARG a 135 *********************** 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 204 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.988 Fit side-chains REVERT: A 24 PHE cc_start: 0.8454 (p90) cc_final: 0.8251 (p90) REVERT: C 58 TYR cc_start: 0.6864 (m-80) cc_final: 0.6648 (m-80) REVERT: a 195 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7476 (tppt) REVERT: b 101 TRP cc_start: 0.7487 (t60) cc_final: 0.7216 (t60) outliers start: 51 outliers final: 36 residues processed: 188 average time/residue: 0.2152 time to fit residues: 55.6042 Evaluate side-chains 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 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 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.203252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171717 restraints weight = 10458.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172213 restraints weight = 10278.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174165 restraints weight = 8665.173| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.209 Angle : 0.630 9.851 12561 Z= 0.308 Chirality : 0.041 0.300 1483 Planarity : 0.006 0.066 1547 Dihedral : 9.352 81.363 1296 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 4.31 % Allowed : 26.91 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1134 helix: 1.09 (0.20), residues: 728 sheet: -2.31 (0.74), residues: 50 loop : -1.33 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 179 HIS 0.003 0.001 HIS C 184 PHE 0.016 0.001 PHE A 24 TYR 0.010 0.001 TYR C 58 ARG 0.007 0.000 ARG a 136 *********************** 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 192 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.861 Fit side-chains REVERT: a 195 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7453 (tppt) REVERT: b 101 TRP cc_start: 0.7414 (t60) cc_final: 0.7127 (t60) outliers start: 40 outliers final: 26 residues processed: 181 average time/residue: 0.1994 time to fit residues: 50.2971 Evaluate side-chains 167 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 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 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 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 219 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN 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 = 0.4350 r_free = 0.4350 target = 0.204526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171306 restraints weight = 10314.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173189 restraints weight = 9206.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174643 restraints weight = 7512.700| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9196 Z= 0.196 Angle : 0.633 8.687 12561 Z= 0.307 Chirality : 0.041 0.240 1483 Planarity : 0.005 0.063 1547 Dihedral : 9.159 80.641 1296 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 5.17 % Allowed : 26.05 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1134 helix: 1.23 (0.20), residues: 728 sheet: -2.21 (0.72), residues: 50 loop : -1.33 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 179 HIS 0.003 0.001 HIS C 6 PHE 0.024 0.001 PHE A 24 TYR 0.010 0.001 TYR C 58 ARG 0.004 0.000 ARG a 136 *********************** 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 192 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.876 Fit side-chains REVERT: C 198 MET cc_start: 0.6097 (tpt) cc_final: 0.5880 (tpt) REVERT: b 101 TRP cc_start: 0.7336 (t60) cc_final: 0.7056 (t60) outliers start: 48 outliers final: 33 residues processed: 178 average time/residue: 0.2029 time to fit residues: 50.1153 Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 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 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 74 MET 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 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 21 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 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 28 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 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 = 0.4316 r_free = 0.4316 target = 0.200867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170457 restraints weight = 10552.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170763 restraints weight = 9200.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171593 restraints weight = 8186.999| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2393 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= 0.247 Angle : 0.671 8.789 12561 Z= 0.326 Chirality : 0.042 0.243 1483 Planarity : 0.005 0.061 1547 Dihedral : 9.066 79.417 1296 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 4.74 % Allowed : 26.80 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1134 helix: 1.06 (0.20), residues: 737 sheet: -2.12 (0.73), residues: 50 loop : -1.38 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.003 0.001 HIS C 184 PHE 0.023 0.001 PHE A 24 TYR 0.013 0.001 TYR C 58 ARG 0.004 0.000 ARG a 136 *********************** 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 187 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.751 Fit side-chains REVERT: C 198 MET cc_start: 0.6244 (tpt) cc_final: 0.5955 (tpt) REVERT: C 221 MET cc_start: 0.7742 (tpt) cc_final: 0.7273 (ttt) REVERT: b 101 TRP cc_start: 0.7514 (t60) cc_final: 0.7185 (t60) outliers start: 44 outliers final: 32 residues processed: 173 average time/residue: 0.1915 time to fit residues: 47.1293 Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 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 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 74 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.202638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.172992 restraints weight = 10540.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172363 restraints weight = 10225.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173963 restraints weight = 9234.941| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9196 Z= 0.217 Angle : 0.655 10.334 12561 Z= 0.317 Chirality : 0.041 0.212 1483 Planarity : 0.005 0.061 1547 Dihedral : 8.965 78.605 1296 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 4.41 % Allowed : 27.23 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1134 helix: 1.19 (0.20), residues: 730 sheet: -1.94 (0.76), residues: 50 loop : -1.25 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.002 0.001 HIS C 184 PHE 0.024 0.001 PHE A 24 TYR 0.016 0.001 TYR B 192 ARG 0.006 0.000 ARG a 146 *********************** 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 185 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.913 Fit side-chains REVERT: A 24 PHE cc_start: 0.8426 (p90) cc_final: 0.8185 (p90) REVERT: B 180 MET cc_start: 0.7705 (ttm) cc_final: 0.7251 (mtp) REVERT: a 16 ARG cc_start: 0.5663 (ttm170) cc_final: 0.4682 (ttp-110) REVERT: a 193 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7663 (mm-30) REVERT: a 195 LYS cc_start: 0.7777 (ptpp) cc_final: 0.7048 (tppt) REVERT: b 101 TRP cc_start: 0.7441 (t60) cc_final: 0.7146 (t60) outliers start: 41 outliers final: 33 residues processed: 175 average time/residue: 0.2028 time to fit residues: 49.5987 Evaluate side-chains 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 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 B residue 181 ASP Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain b residue 74 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 HIS 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 = 0.4359 r_free = 0.4359 target = 0.204869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173397 restraints weight = 10375.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176229 restraints weight = 9896.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177884 restraints weight = 7719.149| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2592 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= 0.198 Angle : 0.643 7.706 12561 Z= 0.311 Chirality : 0.041 0.194 1483 Planarity : 0.005 0.060 1547 Dihedral : 8.827 80.512 1296 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 3.98 % Allowed : 27.99 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1134 helix: 1.20 (0.20), residues: 735 sheet: -1.99 (0.74), residues: 50 loop : -1.20 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.002 0.001 HIS C 60 PHE 0.024 0.001 PHE A 24 TYR 0.016 0.001 TYR B 192 ARG 0.003 0.000 ARG a 136 *********************** 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 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.949 Fit side-chains REVERT: B 129 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6568 (tpt) REVERT: B 180 MET cc_start: 0.7639 (ttm) cc_final: 0.7159 (mtp) REVERT: a 16 ARG cc_start: 0.5849 (ttm170) cc_final: 0.4866 (ttp-110) REVERT: a 193 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7651 (mm-30) REVERT: a 195 LYS cc_start: 0.7751 (ptpp) cc_final: 0.7099 (tppt) REVERT: b 101 TRP cc_start: 0.7428 (t60) cc_final: 0.7089 (t60) outliers start: 37 outliers final: 29 residues processed: 166 average time/residue: 0.2030 time to fit residues: 47.2319 Evaluate side-chains 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 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 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 74 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.202607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171320 restraints weight = 10528.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172927 restraints weight = 9877.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174088 restraints weight = 8567.433| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9196 Z= 0.222 Angle : 0.649 7.695 12561 Z= 0.315 Chirality : 0.041 0.206 1483 Planarity : 0.005 0.060 1547 Dihedral : 8.749 80.372 1296 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 3.34 % Allowed : 28.09 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1134 helix: 1.15 (0.20), residues: 740 sheet: -2.16 (0.71), residues: 50 loop : -1.24 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 66 HIS 0.002 0.001 HIS D 43 PHE 0.025 0.001 PHE A 24 TYR 0.017 0.001 TYR B 192 ARG 0.004 0.000 ARG B 216 ********************** 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 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.012 Fit side-chains REVERT: a 16 ARG cc_start: 0.6072 (ttm170) cc_final: 0.5105 (ttp-110) REVERT: a 193 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7665 (mm-30) REVERT: a 195 LYS cc_start: 0.7784 (ptpp) cc_final: 0.7074 (tppt) REVERT: b 101 TRP cc_start: 0.7439 (t60) cc_final: 0.7117 (t60) outliers start: 31 outliers final: 31 residues processed: 163 average time/residue: 0.2106 time to fit residues: 47.9440 Evaluate side-chains 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 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 43 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 97 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 74 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 115 GLN 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 = 0.4343 r_free = 0.4343 target = 0.203293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171908 restraints weight = 10447.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173647 restraints weight = 9989.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174926 restraints weight = 8206.679| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.207 Angle : 0.652 8.872 12561 Z= 0.313 Chirality : 0.041 0.238 1483 Planarity : 0.005 0.060 1547 Dihedral : 8.715 81.097 1296 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 3.55 % Allowed : 28.31 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1134 helix: 1.20 (0.20), residues: 740 sheet: -2.13 (0.71), residues: 50 loop : -1.23 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.002 0.001 HIS C 184 PHE 0.026 0.001 PHE A 24 TYR 0.017 0.001 TYR B 192 ARG 0.004 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.70 seconds wall clock time: 44 minutes 4.62 seconds (2644.62 seconds total)