Starting phenix.real_space_refine on Wed Apr 30 00:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3v_41013/04_2025/8t3v_41013_neut.cif" } resolution = 3.39 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5562 2.51 5 N 1507 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2061 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'CLR': 1, 'HXA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.65, per 1000 atoms: 0.65 Number of scatterers: 8742 At special positions: 0 Unit cell: (86.73, 120.596, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1621 8.00 N 1507 7.00 C 5562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 170 " distance=2.03 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.657A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 removed outlier: 4.079A pdb=" N GLY A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.632A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.508A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.639A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.020A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.083A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.790A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.722A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.827A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.035A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 225 removed outlier: 3.508A pdb=" N VAL N 225 " --> pdb=" O ALA N 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 3.810A pdb=" N LEU R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS R 33 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 57 Processing helix chain 'R' and resid 57 through 68 removed outlier: 4.203A pdb=" N LEU R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 removed outlier: 4.179A pdb=" N VAL R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.192A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 removed outlier: 3.679A pdb=" N ALA R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE R 117 " --> pdb=" O GLY R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 145 removed outlier: 3.984A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU R 135 " --> pdb=" O TRP R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 removed outlier: 3.583A pdb=" N GLY R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) Proline residue: R 181 - end of helix removed outlier: 3.586A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE R 191 " --> pdb=" O SER R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 212 removed outlier: 3.859A pdb=" N ARG R 211 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 236 removed outlier: 3.654A pdb=" N TRP R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 225 " --> pdb=" O ARG R 221 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 229 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.157A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 244 " --> pdb=" O TYR R 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 245 " --> pdb=" O ASN R 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 248 " --> pdb=" O ASN R 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 267 removed outlier: 3.565A pdb=" N ILE R 263 " --> pdb=" O LYS R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 277 removed outlier: 3.718A pdb=" N LEU R 271 " --> pdb=" O TRP R 267 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.866A pdb=" N GLY R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.705A pdb=" N PHE A 74 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 142 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.421A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.690A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.205A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.416A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.663A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.744A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.706A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG N 98 " --> pdb=" O PHE N 110 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 141 through 142 removed outlier: 3.680A pdb=" N VAL N 156 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 147 through 149 removed outlier: 3.787A pdb=" N GLY N 226 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 176 " --> pdb=" O MET N 231 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1152 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: 2.33 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2820 1.34 - 1.46: 1434 1.46 - 1.58: 4610 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8936 Sorted by residual: bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.09e+01 bond pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N PHE N 68 " pdb=" CA PHE N 68 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.98e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11846 2.53 - 5.07: 264 5.07 - 7.60: 23 7.60 - 10.14: 4 10.14 - 12.67: 1 Bond angle restraints: 12138 Sorted by residual: angle pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 115.25 122.32 -7.07 9.50e-01 1.11e+00 5.54e+01 angle pdb=" O ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 121.96 115.79 6.17 8.40e-01 1.42e+00 5.40e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 110.19 103.47 6.72 1.62e+00 3.81e-01 1.72e+01 angle pdb=" C ARG N 192 " pdb=" N MET N 193 " pdb=" CA MET N 193 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C GLN N 82 " pdb=" N MET N 83 " pdb=" CA MET N 83 " ideal model delta sigma weight residual 121.86 115.34 6.52 1.58e+00 4.01e-01 1.70e+01 ... (remaining 12133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4626 17.81 - 35.63: 532 35.63 - 53.44: 133 53.44 - 71.26: 21 71.26 - 89.07: 3 Dihedral angle restraints: 5315 sinusoidal: 2056 harmonic: 3259 Sorted by residual: dihedral pdb=" C CYS B 233 " pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" CB CYS B 233 " ideal model delta harmonic sigma weight residual -122.60 -113.27 -9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CB CYS N 160 " pdb=" SG CYS N 160 " pdb=" SG CYS N 230 " pdb=" CB CYS N 230 " ideal model delta sinusoidal sigma weight residual 93.00 61.99 31.01 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA MET N 231 " pdb=" C MET N 231 " pdb=" N GLN N 232 " pdb=" CA GLN N 232 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1065 0.053 - 0.106: 225 0.106 - 0.160: 57 0.160 - 0.213: 15 0.213 - 0.266: 6 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LEU B 152 " pdb=" N LEU B 152 " pdb=" C LEU B 152 " pdb=" CB LEU B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 36 " pdb=" N LEU A 36 " pdb=" C LEU A 36 " pdb=" CB LEU A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU N 79 " pdb=" N LEU N 79 " pdb=" C LEU N 79 " pdb=" CB LEU N 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1365 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 HXA R 302 " 0.066 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C16 HXA R 302 " -0.165 2.00e-02 2.50e+03 pdb=" C17 HXA R 302 " 0.164 2.00e-02 2.50e+03 pdb=" C18 HXA R 302 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 302 " 0.109 2.00e-02 2.50e+03 1.10e-01 1.21e+02 pdb=" C4 HXA R 302 " -0.106 2.00e-02 2.50e+03 pdb=" C5 HXA R 302 " -0.114 2.00e-02 2.50e+03 pdb=" C6 HXA R 302 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 302 " -0.041 2.00e-02 2.50e+03 7.44e-02 5.54e+01 pdb=" C7 HXA R 302 " 0.097 2.00e-02 2.50e+03 pdb=" C8 HXA R 302 " -0.097 2.00e-02 2.50e+03 pdb=" C9 HXA R 302 " 0.041 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 397 2.72 - 3.26: 8853 3.26 - 3.81: 14304 3.81 - 4.35: 17536 4.35 - 4.90: 29965 Nonbonded interactions: 71055 Sorted by model distance: nonbonded pdb=" O TYR R 240 " pdb=" OG SER R 243 " model vdw 2.175 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.229 3.040 nonbonded pdb=" NH1 ARG A 93 " pdb=" OD1 ASP A 124 " model vdw 2.279 3.120 nonbonded pdb=" O THR B 47 " pdb=" OG1 THR B 47 " model vdw 2.286 3.040 ... (remaining 71050 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.320 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 23.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.005 0.044 8939 Z= 0.328 Angle : 0.809 12.674 12144 Z= 0.509 Chirality : 0.053 0.266 1368 Planarity : 0.007 0.125 1555 Dihedral : 15.857 89.070 3214 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.44 % Allowed : 25.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1120 helix: 1.36 (0.28), residues: 350 sheet: -0.41 (0.32), residues: 263 loop : -0.03 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS R 216 PHE 0.020 0.001 PHE B 151 TYR 0.017 0.001 TYR B 59 ARG 0.007 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.24081 ( 404) hydrogen bonds : angle 8.23452 ( 1152) SS BOND : bond 0.00465 ( 3) SS BOND : angle 1.58174 ( 6) covalent geometry : bond 0.00472 ( 8936) covalent geometry : angle 0.80831 (12138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7495 (m-80) cc_final: 0.7010 (m-80) REVERT: B 217 MET cc_start: 0.6921 (tpt) cc_final: 0.6685 (tpt) REVERT: N 34 MET cc_start: 0.4780 (mmt) cc_final: 0.4238 (mmt) REVERT: N 76 LYS cc_start: 0.7339 (mtpp) cc_final: 0.6758 (mppt) REVERT: N 173 THR cc_start: 0.4018 (m) cc_final: 0.3806 (m) REVERT: R 8 SER cc_start: 0.7843 (m) cc_final: 0.7388 (t) REVERT: R 35 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5725 (mmp-170) outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.2200 time to fit residues: 69.4520 Evaluate side-chains 172 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 168 HIS N 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.184810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134697 restraints weight = 10586.275| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.11 r_work: 0.3426 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8939 Z= 0.178 Angle : 0.678 14.021 12144 Z= 0.345 Chirality : 0.045 0.165 1368 Planarity : 0.005 0.054 1555 Dihedral : 5.098 41.777 1312 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.59 % Allowed : 22.82 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.25), residues: 1120 helix: 1.44 (0.28), residues: 360 sheet: -0.45 (0.33), residues: 248 loop : 0.01 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 297 HIS 0.008 0.002 HIS B 62 PHE 0.028 0.002 PHE B 199 TYR 0.020 0.002 TYR B 59 ARG 0.004 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 404) hydrogen bonds : angle 5.31769 ( 1152) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.07457 ( 6) covalent geometry : bond 0.00406 ( 8936) covalent geometry : angle 0.67756 (12138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6632 (ptt) REVERT: A 53 MET cc_start: 0.6875 (tmm) cc_final: 0.6575 (tmm) REVERT: A 77 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: A 124 ASP cc_start: 0.8497 (t0) cc_final: 0.8122 (t70) REVERT: B 57 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8209 (pttm) REVERT: B 124 TYR cc_start: 0.8621 (m-80) cc_final: 0.8240 (m-80) REVERT: B 261 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 322 ASP cc_start: 0.8234 (t0) cc_final: 0.8021 (t0) REVERT: B 334 SER cc_start: 0.8302 (p) cc_final: 0.8048 (t) REVERT: N 71 SER cc_start: 0.7822 (p) cc_final: 0.7542 (m) REVERT: N 76 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6932 (mppt) REVERT: N 141 MET cc_start: 0.7648 (tpp) cc_final: 0.7425 (tpt) REVERT: N 227 VAL cc_start: 0.6287 (OUTLIER) cc_final: 0.6047 (t) REVERT: R 28 ARG cc_start: 0.8231 (tmt-80) cc_final: 0.7498 (mmm160) REVERT: R 74 LEU cc_start: 0.8258 (mm) cc_final: 0.7892 (tp) REVERT: R 184 PHE cc_start: 0.6521 (t80) cc_final: 0.6293 (t80) REVERT: R 241 ASN cc_start: 0.7757 (t0) cc_final: 0.7543 (t0) outliers start: 42 outliers final: 19 residues processed: 209 average time/residue: 0.1744 time to fit residues: 52.5187 Evaluate side-chains 172 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.178407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122059 restraints weight = 10694.490| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.21 r_work: 0.3340 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8939 Z= 0.158 Angle : 0.634 11.662 12144 Z= 0.320 Chirality : 0.044 0.171 1368 Planarity : 0.004 0.048 1555 Dihedral : 5.019 50.997 1312 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.37 % Allowed : 24.56 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.55 (0.26), residues: 1120 helix: 1.70 (0.28), residues: 365 sheet: -0.51 (0.31), residues: 267 loop : -0.02 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.025 0.002 HIS N 168 PHE 0.019 0.002 PHE N 213 TYR 0.018 0.002 TYR B 59 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 404) hydrogen bonds : angle 4.83087 ( 1152) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.60546 ( 6) covalent geometry : bond 0.00360 ( 8936) covalent geometry : angle 0.63435 (12138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6532 (tmm) REVERT: A 196 GLU cc_start: 0.7639 (tt0) cc_final: 0.7360 (tt0) REVERT: B 57 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8276 (pttm) REVERT: B 66 ASP cc_start: 0.8274 (t0) cc_final: 0.7898 (t0) REVERT: B 124 TYR cc_start: 0.8895 (m-80) cc_final: 0.8463 (m-80) REVERT: B 129 ARG cc_start: 0.8305 (mmm160) cc_final: 0.8085 (mmm160) REVERT: B 322 ASP cc_start: 0.8431 (t0) cc_final: 0.8119 (t0) REVERT: N 39 GLN cc_start: 0.7245 (tt0) cc_final: 0.6938 (tt0) REVERT: N 76 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7119 (mppt) REVERT: R 35 ARG cc_start: 0.6429 (mmm160) cc_final: 0.5417 (mmp-170) REVERT: R 119 ARG cc_start: 0.6877 (mtp180) cc_final: 0.6622 (mtm-85) REVERT: R 253 LEU cc_start: 0.7881 (tt) cc_final: 0.7305 (mt) outliers start: 40 outliers final: 20 residues processed: 203 average time/residue: 0.2181 time to fit residues: 60.3886 Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.174142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118134 restraints weight = 10589.443| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.15 r_work: 0.3309 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8939 Z= 0.175 Angle : 0.633 13.188 12144 Z= 0.316 Chirality : 0.044 0.281 1368 Planarity : 0.004 0.039 1555 Dihedral : 4.946 49.178 1312 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.15 % Allowed : 25.00 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.61 (0.26), residues: 1120 helix: 1.83 (0.28), residues: 359 sheet: -0.53 (0.31), residues: 286 loop : 0.04 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.015 0.002 HIS B 311 PHE 0.019 0.002 PHE B 199 TYR 0.019 0.002 TYR B 59 ARG 0.006 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 404) hydrogen bonds : angle 4.65696 ( 1152) SS BOND : bond 0.00458 ( 3) SS BOND : angle 0.84997 ( 6) covalent geometry : bond 0.00406 ( 8936) covalent geometry : angle 0.63253 (12138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6585 (tmt) REVERT: A 166 GLU cc_start: 0.8018 (pm20) cc_final: 0.7177 (tp30) REVERT: B 124 TYR cc_start: 0.8983 (m-80) cc_final: 0.8762 (m-80) REVERT: B 170 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 259 GLN cc_start: 0.8542 (pt0) cc_final: 0.7908 (pt0) REVERT: B 322 ASP cc_start: 0.8237 (t0) cc_final: 0.7846 (t0) REVERT: N 39 GLN cc_start: 0.8079 (tt0) cc_final: 0.7801 (tt0) REVERT: N 73 ASP cc_start: 0.7126 (t70) cc_final: 0.6696 (t70) REVERT: N 76 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7239 (mppt) REVERT: N 83 MET cc_start: 0.7802 (mmm) cc_final: 0.7602 (mmm) REVERT: N 232 GLN cc_start: 0.7958 (pp30) cc_final: 0.7701 (pp30) REVERT: R 35 ARG cc_start: 0.6576 (mmm160) cc_final: 0.5475 (mmp-170) REVERT: R 253 LEU cc_start: 0.7842 (tt) cc_final: 0.7408 (mt) outliers start: 38 outliers final: 27 residues processed: 192 average time/residue: 0.2109 time to fit residues: 55.2348 Evaluate side-chains 183 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 276 THR Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 168 HIS R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120742 restraints weight = 10598.713| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.11 r_work: 0.3345 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8939 Z= 0.120 Angle : 0.589 12.174 12144 Z= 0.291 Chirality : 0.042 0.211 1368 Planarity : 0.004 0.037 1555 Dihedral : 4.812 58.687 1312 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.60 % Allowed : 26.42 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.73 (0.26), residues: 1120 helix: 1.96 (0.28), residues: 361 sheet: -0.46 (0.30), residues: 288 loop : 0.08 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 PHE 0.022 0.002 PHE R 82 TYR 0.020 0.001 TYR N 191 ARG 0.004 0.000 ARG R 119 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 404) hydrogen bonds : angle 4.42233 ( 1152) SS BOND : bond 0.00383 ( 3) SS BOND : angle 0.67636 ( 6) covalent geometry : bond 0.00276 ( 8936) covalent geometry : angle 0.58926 (12138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8127 (t0) cc_final: 0.7783 (m-30) REVERT: A 117 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7592 (mtp180) REVERT: A 243 TYR cc_start: 0.8345 (m-80) cc_final: 0.8115 (m-80) REVERT: B 170 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 259 GLN cc_start: 0.8450 (pt0) cc_final: 0.8207 (pt0) REVERT: B 311 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.8200 (t-90) REVERT: B 322 ASP cc_start: 0.8351 (t0) cc_final: 0.7847 (t0) REVERT: N 39 GLN cc_start: 0.8061 (tt0) cc_final: 0.7794 (tt0) REVERT: N 76 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7396 (mppt) REVERT: N 83 MET cc_start: 0.8082 (mmm) cc_final: 0.7812 (mmt) REVERT: N 231 MET cc_start: 0.7709 (mtm) cc_final: 0.7499 (ttp) REVERT: R 28 ARG cc_start: 0.8275 (tmt-80) cc_final: 0.6425 (mmp-170) REVERT: R 35 ARG cc_start: 0.6606 (mmm160) cc_final: 0.5511 (mmp-170) REVERT: R 253 LEU cc_start: 0.7795 (tt) cc_final: 0.7326 (mt) outliers start: 33 outliers final: 19 residues processed: 189 average time/residue: 0.2583 time to fit residues: 64.6537 Evaluate side-chains 175 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122938 restraints weight = 10501.459| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.31 r_work: 0.3319 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8939 Z= 0.128 Angle : 0.597 13.694 12144 Z= 0.292 Chirality : 0.042 0.196 1368 Planarity : 0.004 0.036 1555 Dihedral : 4.775 58.955 1312 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.69 % Allowed : 25.33 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.79 (0.26), residues: 1120 helix: 2.03 (0.28), residues: 362 sheet: -0.31 (0.31), residues: 273 loop : -0.02 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.006 0.001 HIS R 216 PHE 0.020 0.002 PHE R 16 TYR 0.019 0.001 TYR N 191 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 404) hydrogen bonds : angle 4.30013 ( 1152) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.62861 ( 6) covalent geometry : bond 0.00297 ( 8936) covalent geometry : angle 0.59657 (12138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6522 (tmt) REVERT: A 143 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 166 GLU cc_start: 0.7959 (pm20) cc_final: 0.7401 (tp30) REVERT: A 243 TYR cc_start: 0.8336 (m-80) cc_final: 0.8077 (m-80) REVERT: A 244 ASN cc_start: 0.8552 (m-40) cc_final: 0.7982 (t0) REVERT: B 153 ASP cc_start: 0.7686 (m-30) cc_final: 0.7297 (m-30) REVERT: B 170 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: B 198 LEU cc_start: 0.8723 (mp) cc_final: 0.8486 (mt) REVERT: B 259 GLN cc_start: 0.8441 (pt0) cc_final: 0.8223 (pt0) REVERT: B 311 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.8115 (t-90) REVERT: B 322 ASP cc_start: 0.8218 (t0) cc_final: 0.7792 (t0) REVERT: N 39 GLN cc_start: 0.8090 (tt0) cc_final: 0.7824 (tt0) REVERT: N 76 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7428 (mppt) REVERT: R 28 ARG cc_start: 0.8287 (tmt-80) cc_final: 0.6479 (mmp-170) REVERT: R 35 ARG cc_start: 0.6713 (mmm160) cc_final: 0.5610 (mmp-170) REVERT: R 119 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.7006 (mtm110) REVERT: R 253 LEU cc_start: 0.7806 (tt) cc_final: 0.7311 (mt) outliers start: 43 outliers final: 29 residues processed: 191 average time/residue: 0.2388 time to fit residues: 61.7780 Evaluate side-chains 184 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 168 HIS N 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121476 restraints weight = 10585.048| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.10 r_work: 0.3346 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8939 Z= 0.117 Angle : 0.589 13.723 12144 Z= 0.289 Chirality : 0.042 0.166 1368 Planarity : 0.004 0.033 1555 Dihedral : 4.652 55.065 1312 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.15 % Allowed : 25.66 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.89 (0.26), residues: 1120 helix: 2.08 (0.28), residues: 363 sheet: -0.20 (0.32), residues: 267 loop : 0.02 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 PHE 0.016 0.001 PHE N 213 TYR 0.019 0.001 TYR N 191 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 404) hydrogen bonds : angle 4.22136 ( 1152) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.51638 ( 6) covalent geometry : bond 0.00265 ( 8936) covalent geometry : angle 0.58919 (12138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6519 (tmt) REVERT: A 143 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 166 GLU cc_start: 0.8028 (pm20) cc_final: 0.7382 (tp30) REVERT: A 243 TYR cc_start: 0.8295 (m-80) cc_final: 0.8019 (m-80) REVERT: A 244 ASN cc_start: 0.8559 (m-40) cc_final: 0.7980 (t0) REVERT: B 153 ASP cc_start: 0.7671 (m-30) cc_final: 0.7306 (m-30) REVERT: B 170 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: B 198 LEU cc_start: 0.8718 (mp) cc_final: 0.8477 (mt) REVERT: B 266 HIS cc_start: 0.8806 (t-90) cc_final: 0.8548 (t-90) REVERT: B 311 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8101 (t-90) REVERT: B 322 ASP cc_start: 0.8287 (t0) cc_final: 0.7795 (t0) REVERT: N 39 GLN cc_start: 0.8059 (tt0) cc_final: 0.7830 (tt0) REVERT: N 76 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7375 (mppt) REVERT: R 9 PHE cc_start: 0.8357 (t80) cc_final: 0.8052 (t80) REVERT: R 28 ARG cc_start: 0.8233 (tmt-80) cc_final: 0.6403 (mmp-170) REVERT: R 35 ARG cc_start: 0.6769 (mmm160) cc_final: 0.5652 (mmp-170) REVERT: R 119 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6899 (mtm180) REVERT: R 253 LEU cc_start: 0.7788 (tt) cc_final: 0.7355 (mt) outliers start: 38 outliers final: 24 residues processed: 183 average time/residue: 0.2263 time to fit residues: 56.1915 Evaluate side-chains 182 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 168 HIS N 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116675 restraints weight = 10832.913| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.15 r_work: 0.3252 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.8314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8939 Z= 0.187 Angle : 0.639 12.854 12144 Z= 0.318 Chirality : 0.045 0.258 1368 Planarity : 0.004 0.033 1555 Dihedral : 4.962 57.764 1312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.59 % Allowed : 25.66 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.72 (0.26), residues: 1120 helix: 1.94 (0.28), residues: 362 sheet: -0.41 (0.31), residues: 272 loop : 0.01 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.005 0.001 HIS R 216 PHE 0.014 0.002 PHE R 82 TYR 0.023 0.002 TYR B 59 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 404) hydrogen bonds : angle 4.38155 ( 1152) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.57521 ( 6) covalent geometry : bond 0.00437 ( 8936) covalent geometry : angle 0.63884 (12138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6533 (tmt) REVERT: A 117 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6627 (ttp80) REVERT: A 126 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7971 (tttm) REVERT: A 143 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 166 GLU cc_start: 0.8062 (pm20) cc_final: 0.7414 (tp30) REVERT: A 244 ASN cc_start: 0.8594 (m-40) cc_final: 0.8035 (t0) REVERT: B 153 ASP cc_start: 0.7726 (m-30) cc_final: 0.7372 (m-30) REVERT: B 170 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 198 LEU cc_start: 0.8615 (mp) cc_final: 0.8321 (mt) REVERT: B 246 ASP cc_start: 0.8557 (t0) cc_final: 0.8265 (m-30) REVERT: B 259 GLN cc_start: 0.8494 (pt0) cc_final: 0.7947 (pt0) REVERT: B 266 HIS cc_start: 0.8835 (t-90) cc_final: 0.8463 (t-90) REVERT: B 311 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8030 (t-90) REVERT: B 322 ASP cc_start: 0.8248 (t0) cc_final: 0.7835 (t0) REVERT: G 62 ARG cc_start: 0.7094 (ptp-110) cc_final: 0.6868 (ptp-110) REVERT: N 39 GLN cc_start: 0.8342 (tt0) cc_final: 0.8065 (tt0) REVERT: R 9 PHE cc_start: 0.8454 (t80) cc_final: 0.8125 (t80) REVERT: R 28 ARG cc_start: 0.8269 (tmt-80) cc_final: 0.6518 (mmt180) REVERT: R 35 ARG cc_start: 0.6759 (mmm160) cc_final: 0.5672 (mmp-170) REVERT: R 90 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7633 (mp) REVERT: R 119 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.7016 (mtm110) REVERT: R 250 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: R 253 LEU cc_start: 0.7879 (tt) cc_final: 0.7452 (mt) outliers start: 42 outliers final: 27 residues processed: 194 average time/residue: 0.2188 time to fit residues: 57.8334 Evaluate side-chains 194 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 168 HIS N 180 GLN R 47 ASN R 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.173830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118801 restraints weight = 10602.374| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.95 r_work: 0.3314 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.8449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8939 Z= 0.124 Angle : 0.608 13.424 12144 Z= 0.296 Chirality : 0.043 0.167 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.756 52.811 1312 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.71 % Allowed : 26.42 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.83 (0.26), residues: 1120 helix: 2.04 (0.28), residues: 362 sheet: -0.29 (0.32), residues: 270 loop : 0.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 PHE 0.024 0.001 PHE R 16 TYR 0.019 0.001 TYR B 59 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 404) hydrogen bonds : angle 4.22767 ( 1152) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.46192 ( 6) covalent geometry : bond 0.00285 ( 8936) covalent geometry : angle 0.60842 (12138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6401 (tmt) REVERT: A 117 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6520 (ttp80) REVERT: A 143 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 151 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: A 166 GLU cc_start: 0.8046 (pm20) cc_final: 0.7414 (tp30) REVERT: A 212 TYR cc_start: 0.8938 (m-80) cc_final: 0.8667 (m-10) REVERT: A 230 ASP cc_start: 0.8481 (m-30) cc_final: 0.8006 (m-30) REVERT: A 243 TYR cc_start: 0.8261 (m-80) cc_final: 0.7999 (m-80) REVERT: A 244 ASN cc_start: 0.8534 (m-40) cc_final: 0.7989 (t0) REVERT: B 153 ASP cc_start: 0.7702 (m-30) cc_final: 0.7325 (m-30) REVERT: B 170 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: B 198 LEU cc_start: 0.8561 (mp) cc_final: 0.8291 (mt) REVERT: B 246 ASP cc_start: 0.8498 (t0) cc_final: 0.8220 (m-30) REVERT: B 266 HIS cc_start: 0.8834 (t-90) cc_final: 0.8505 (t-170) REVERT: B 311 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.8052 (t-90) REVERT: B 322 ASP cc_start: 0.8347 (t0) cc_final: 0.7848 (t0) REVERT: N 5 VAL cc_start: 0.8469 (t) cc_final: 0.8249 (p) REVERT: N 19 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7840 (tptm) REVERT: N 39 GLN cc_start: 0.8252 (tt0) cc_final: 0.8019 (tt0) REVERT: R 9 PHE cc_start: 0.8464 (t80) cc_final: 0.8115 (t80) REVERT: R 28 ARG cc_start: 0.8166 (tmt-80) cc_final: 0.6374 (mmt180) REVERT: R 35 ARG cc_start: 0.6770 (mmm160) cc_final: 0.5697 (mmp-170) REVERT: R 90 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7563 (mp) REVERT: R 119 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6944 (mtm110) REVERT: R 250 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: R 253 LEU cc_start: 0.7853 (tt) cc_final: 0.7424 (mt) outliers start: 34 outliers final: 21 residues processed: 186 average time/residue: 0.2235 time to fit residues: 55.9384 Evaluate side-chains 185 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0980 chunk 73 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.177396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122590 restraints weight = 10596.942| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.97 r_work: 0.3369 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.8583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8939 Z= 0.106 Angle : 0.590 13.281 12144 Z= 0.287 Chirality : 0.041 0.153 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.480 47.212 1312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.95 % Allowed : 27.62 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.01 (0.26), residues: 1120 helix: 2.17 (0.28), residues: 364 sheet: -0.10 (0.33), residues: 260 loop : 0.07 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 PHE 0.023 0.001 PHE R 16 TYR 0.018 0.001 TYR N 191 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 404) hydrogen bonds : angle 4.05647 ( 1152) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.44732 ( 6) covalent geometry : bond 0.00235 ( 8936) covalent geometry : angle 0.59045 (12138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6833 (tmm) cc_final: 0.6409 (tmt) REVERT: A 143 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 151 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: A 166 GLU cc_start: 0.8063 (pm20) cc_final: 0.7428 (tp30) REVERT: A 230 ASP cc_start: 0.8364 (m-30) cc_final: 0.8000 (m-30) REVERT: A 243 TYR cc_start: 0.8172 (m-80) cc_final: 0.7947 (m-80) REVERT: A 244 ASN cc_start: 0.8452 (m-40) cc_final: 0.7966 (t0) REVERT: B 153 ASP cc_start: 0.7703 (m-30) cc_final: 0.7326 (m-30) REVERT: B 170 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: B 198 LEU cc_start: 0.8601 (mp) cc_final: 0.8350 (mt) REVERT: B 214 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8701 (ptp-170) REVERT: B 266 HIS cc_start: 0.8793 (t-90) cc_final: 0.8508 (t-170) REVERT: B 311 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8045 (t-90) REVERT: N 19 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7714 (tptp) REVERT: N 39 GLN cc_start: 0.8100 (tt0) cc_final: 0.7897 (tt0) REVERT: N 221 GLU cc_start: 0.7154 (mp0) cc_final: 0.6659 (mp0) REVERT: R 9 PHE cc_start: 0.8435 (t80) cc_final: 0.8064 (t80) REVERT: R 28 ARG cc_start: 0.8082 (tmt-80) cc_final: 0.7373 (ttp-170) REVERT: R 35 ARG cc_start: 0.6795 (mmm160) cc_final: 0.5769 (mmp-170) REVERT: R 250 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: R 253 LEU cc_start: 0.7818 (tt) cc_final: 0.7472 (mt) outliers start: 27 outliers final: 16 residues processed: 182 average time/residue: 0.2189 time to fit residues: 54.4332 Evaluate side-chains 177 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 250 TYR Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 60 optimal weight: 0.0770 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 168 HIS ** R 272 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 = 0.4135 r_free = 0.4135 target = 0.177665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122970 restraints weight = 10611.518| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.98 r_work: 0.3369 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.8668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8939 Z= 0.107 Angle : 0.595 13.173 12144 Z= 0.288 Chirality : 0.042 0.149 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.400 45.498 1312 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.84 % Allowed : 28.71 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.00 (0.26), residues: 1120 helix: 2.23 (0.28), residues: 364 sheet: -0.39 (0.32), residues: 279 loop : 0.23 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 PHE 0.014 0.001 PHE R 82 TYR 0.016 0.001 TYR N 191 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 404) hydrogen bonds : angle 4.06415 ( 1152) SS BOND : bond 0.00283 ( 3) SS BOND : angle 0.43654 ( 6) covalent geometry : bond 0.00241 ( 8936) covalent geometry : angle 0.59484 (12138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4717.00 seconds wall clock time: 82 minutes 53.15 seconds (4973.15 seconds total)