Starting phenix.real_space_refine on Sat Dec 28 17:37:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce5_16599/12_2024/8ce5_16599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce5_16599/12_2024/8ce5_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_16599/12_2024/8ce5_16599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce5_16599/12_2024/8ce5_16599.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce5_16599/12_2024/8ce5_16599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce5_16599/12_2024/8ce5_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-5532/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: 5.80, per 1000 atoms: 0.65 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: 2.50 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: 0.80 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: 2.20 Time building geometry restraints manager: 2.84 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: 1.130 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- 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 : 1.044 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: 44.9817 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 : 1.035 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 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 : 1.336 Fit side-chains REVERT: A 91 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 85 LEU cc_start: 0.7504 (mt) cc_final: 0.7141 (mt) REVERT: a 156 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: a 195 LYS cc_start: 0.7553 (ptpp) cc_final: 0.6954 (tppt) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 0.2209 time to fit residues: 53.9940 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 : 0.989 ------------------------------------------------------------------------------- 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 56 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1634 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= 0.293 Angle : 0.681 8.052 12561 Z= 0.334 Chirality : 0.043 0.255 1483 Planarity : 0.006 0.078 1547 Dihedral : 9.722 81.193 1296 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 4.09 % Allowed : 24.65 % 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 (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: -0.38 (0.25), residues: 1134 helix: 0.64 (0.20), residues: 721 sheet: -2.66 (0.69), residues: 50 loop : -1.62 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 180 HIS 0.004 0.001 HIS D 43 PHE 0.013 0.001 PHE a 156 TYR 0.016 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 188 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: B 2 MET cc_start: 0.6969 (tpp) cc_final: 0.6540 (tpp) REVERT: C 179 TRP cc_start: 0.7763 (t60) cc_final: 0.7022 (t60) REVERT: a 195 LYS cc_start: 0.7592 (ptpp) cc_final: 0.6990 (tppt) REVERT: b 42 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: b 101 TRP cc_start: 0.7464 (t60) cc_final: 0.7229 (t60) outliers start: 38 outliers final: 27 residues processed: 178 average time/residue: 0.2153 time to fit residues: 52.9224 Evaluate side-chains 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 25 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 23 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 76 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1989 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= 0.264 Angle : 0.654 7.307 12561 Z= 0.321 Chirality : 0.042 0.204 1483 Planarity : 0.006 0.072 1547 Dihedral : 9.514 81.181 1296 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 5.38 % Allowed : 25.08 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.25), residues: 1134 helix: 0.83 (0.20), residues: 730 sheet: -2.39 (0.73), residues: 50 loop : -1.51 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 66 HIS 0.003 0.001 HIS D 38 PHE 0.012 0.001 PHE a 156 TYR 0.024 0.002 TYR B 192 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 203 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 2 MET cc_start: 0.6863 (tpp) cc_final: 0.6427 (tpp) REVERT: C 58 TYR cc_start: 0.6881 (m-80) cc_final: 0.6650 (m-80) REVERT: a 193 GLU cc_start: 0.7840 (tp30) cc_final: 0.7489 (tp30) REVERT: a 195 LYS cc_start: 0.7671 (ptpp) cc_final: 0.7034 (tppt) REVERT: b 101 TRP cc_start: 0.7536 (t60) cc_final: 0.7270 (t60) outliers start: 50 outliers final: 34 residues processed: 187 average time/residue: 0.2158 time to fit residues: 55.6537 Evaluate side-chains 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 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 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 61 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2211 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= 0.253 Angle : 0.654 10.224 12561 Z= 0.319 Chirality : 0.043 0.317 1483 Planarity : 0.006 0.067 1547 Dihedral : 9.419 81.062 1296 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 5.60 % Allowed : 25.94 % 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: 0.03 (0.26), residues: 1134 helix: 0.93 (0.20), residues: 730 sheet: -2.26 (0.75), residues: 50 loop : -1.50 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 66 HIS 0.003 0.001 HIS D 38 PHE 0.022 0.001 PHE A 24 TYR 0.025 0.002 TYR B 192 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 203 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 MET cc_start: 0.7745 (tpt) cc_final: 0.7370 (ttt) REVERT: a 193 GLU cc_start: 0.7785 (tp30) cc_final: 0.7393 (tp30) REVERT: a 195 LYS cc_start: 0.7655 (ptpp) cc_final: 0.7058 (tppt) REVERT: b 101 TRP cc_start: 0.7508 (t60) cc_final: 0.7240 (t60) outliers start: 52 outliers final: 38 residues processed: 190 average time/residue: 0.2121 time to fit residues: 56.3238 Evaluate side-chains 181 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU 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 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 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 D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2489 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= 0.275 Angle : 0.673 8.921 12561 Z= 0.326 Chirality : 0.043 0.299 1483 Planarity : 0.006 0.063 1547 Dihedral : 9.287 80.079 1296 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 6.67 % Allowed : 26.05 % 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 (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 (0.26), residues: 1134 helix: 0.87 (0.20), residues: 738 sheet: -2.40 (0.71), residues: 50 loop : -1.41 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 179 HIS 0.006 0.001 HIS C 6 PHE 0.022 0.002 PHE A 24 TYR 0.017 0.002 TYR B 192 ARG 0.005 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 206 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.985 Fit side-chains REVERT: A 3 MET cc_start: 0.7835 (mmt) cc_final: 0.7617 (tpp) REVERT: C 80 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8061 (tp) REVERT: C 221 MET cc_start: 0.7795 (tpt) cc_final: 0.7396 (ttt) REVERT: a 49 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7876 (mp) REVERT: a 193 GLU cc_start: 0.7729 (tp30) cc_final: 0.7337 (tp30) REVERT: a 195 LYS cc_start: 0.7676 (ptpp) cc_final: 0.7089 (tppt) REVERT: b 101 TRP cc_start: 0.7520 (t60) cc_final: 0.7242 (t60) outliers start: 62 outliers final: 37 residues processed: 185 average time/residue: 0.2121 time to fit residues: 54.2790 Evaluate side-chains 177 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 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 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9196 Z= 0.407 Angle : 0.781 8.735 12561 Z= 0.379 Chirality : 0.047 0.345 1483 Planarity : 0.006 0.064 1547 Dihedral : 9.332 79.096 1296 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 6.78 % Allowed : 25.62 % 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 (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: -0.27 (0.25), residues: 1134 helix: 0.63 (0.19), residues: 731 sheet: -2.65 (0.70), residues: 50 loop : -1.38 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 66 HIS 0.005 0.001 HIS C 184 PHE 0.022 0.002 PHE A 24 TYR 0.021 0.002 TYR B 192 ARG 0.004 0.001 ARG a 135 *********************** 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 210 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 1.009 Fit side-chains REVERT: C 59 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 80 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 221 MET cc_start: 0.7798 (tpt) cc_final: 0.7402 (ttt) REVERT: a 16 ARG cc_start: 0.6027 (ttm170) cc_final: 0.4964 (ttp-110) REVERT: a 49 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7805 (mp) REVERT: a 156 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: a 193 GLU cc_start: 0.7712 (tp30) cc_final: 0.7344 (tp30) REVERT: b 101 TRP cc_start: 0.7750 (t60) cc_final: 0.7509 (t60) outliers start: 63 outliers final: 42 residues processed: 190 average time/residue: 0.2141 time to fit residues: 56.7683 Evaluate side-chains 185 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 93 VAL 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 181 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 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 23 SER Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Chi-restraints excluded: chain b residue 219 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9196 Z= 0.219 Angle : 0.669 9.355 12561 Z= 0.328 Chirality : 0.042 0.232 1483 Planarity : 0.006 0.062 1547 Dihedral : 9.210 78.511 1296 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 4.31 % Allowed : 28.31 % 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 (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: 0.17 (0.26), residues: 1134 helix: 1.02 (0.20), residues: 732 sheet: -2.46 (0.71), residues: 50 loop : -1.35 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 126 HIS 0.003 0.001 HIS D 38 PHE 0.025 0.001 PHE A 24 TYR 0.021 0.002 TYR B 192 ARG 0.006 0.000 ARG C 153 *********************** 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 182 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: C 221 MET cc_start: 0.7760 (tpt) cc_final: 0.7338 (ttt) REVERT: a 16 ARG cc_start: 0.6132 (ttm170) cc_final: 0.5071 (ttp-110) REVERT: a 49 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7788 (mp) REVERT: a 193 GLU cc_start: 0.7761 (tp30) cc_final: 0.7389 (tp30) REVERT: b 101 TRP cc_start: 0.7539 (t60) cc_final: 0.7287 (t60) outliers start: 40 outliers final: 28 residues processed: 169 average time/residue: 0.2052 time to fit residues: 48.2316 Evaluate side-chains 166 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 C residue 43 PHE Chi-restraints excluded: chain C residue 67 SER 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 5 GLU 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 171 MET Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9196 Z= 0.298 Angle : 0.706 7.712 12561 Z= 0.345 Chirality : 0.044 0.269 1483 Planarity : 0.006 0.061 1547 Dihedral : 9.094 76.869 1296 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 3.98 % Allowed : 28.96 % 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 (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: -0.02 (0.25), residues: 1134 helix: 0.85 (0.19), residues: 734 sheet: -2.34 (0.73), residues: 50 loop : -1.42 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 179 HIS 0.003 0.001 HIS a 83 PHE 0.024 0.002 PHE A 24 TYR 0.023 0.002 TYR C 58 ARG 0.004 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 : 1.130 Fit side-chains revert: symmetry clash REVERT: C 221 MET cc_start: 0.7762 (tpt) cc_final: 0.7344 (ttt) REVERT: a 16 ARG cc_start: 0.6302 (ttm170) cc_final: 0.5262 (ttp-110) REVERT: a 193 GLU cc_start: 0.7747 (tp30) cc_final: 0.7239 (tp30) REVERT: a 195 LYS cc_start: 0.7608 (ptpp) cc_final: 0.6566 (tppt) REVERT: b 101 TRP cc_start: 0.7666 (t60) cc_final: 0.7371 (t60) outliers start: 37 outliers final: 31 residues processed: 163 average time/residue: 0.2375 time to fit residues: 54.2260 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 23 SER Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 a 186 HIS a 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 0.044 9196 Z= 0.224 Angle : 0.676 10.398 12561 Z= 0.328 Chirality : 0.043 0.313 1483 Planarity : 0.006 0.061 1547 Dihedral : 9.027 78.587 1296 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 3.66 % Allowed : 29.49 % Favored : 66.85 % 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: 0.20 (0.26), residues: 1134 helix: 1.02 (0.20), residues: 740 sheet: -2.29 (0.72), residues: 50 loop : -1.37 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 126 HIS 0.002 0.001 HIS a 83 PHE 0.026 0.001 PHE A 24 TYR 0.022 0.001 TYR C 58 ARG 0.003 0.000 ARG a 146 ********************** 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 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.070 Fit side-chains REVERT: B 180 MET cc_start: 0.7700 (ttm) cc_final: 0.7247 (mtp) REVERT: C 221 MET cc_start: 0.7731 (tpt) cc_final: 0.7330 (ttt) REVERT: a 16 ARG cc_start: 0.6225 (ttm170) cc_final: 0.5223 (ttp-110) REVERT: a 49 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7795 (mp) REVERT: a 80 TRP cc_start: 0.8498 (t-100) cc_final: 0.8135 (t60) REVERT: a 193 GLU cc_start: 0.7727 (tp30) cc_final: 0.7197 (tp30) REVERT: a 195 LYS cc_start: 0.7608 (ptpp) cc_final: 0.6691 (tppt) REVERT: b 101 TRP cc_start: 0.7596 (t60) cc_final: 0.7319 (t60) outliers start: 34 outliers final: 31 residues processed: 158 average time/residue: 0.2219 time to fit residues: 48.8308 Evaluate side-chains 169 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 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 67 SER 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 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 189 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155163 restraints weight = 9577.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156437 restraints weight = 9909.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157773 restraints weight = 7917.673| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9196 Z= 0.390 Angle : 0.787 11.797 12561 Z= 0.380 Chirality : 0.047 0.394 1483 Planarity : 0.006 0.061 1547 Dihedral : 9.029 75.183 1296 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.20 % Favored : 94.62 % Rotamer: Outliers : 3.44 % Allowed : 30.03 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.25), residues: 1134 helix: 0.75 (0.19), residues: 734 sheet: -2.34 (0.72), residues: 48 loop : -1.41 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 126 HIS 0.005 0.001 HIS a 83 PHE 0.029 0.002 PHE b 28 TYR 0.028 0.002 TYR C 58 ARG 0.004 0.001 ARG a 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.99 seconds wall clock time: 33 minutes 8.91 seconds (1988.91 seconds total)