Starting phenix.real_space_refine on Fri Jul 19 21:48:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_41013_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_41013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_41013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_41013_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3v_41013/07_2024/8t3v_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 Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "N ARG 219": "NH1" <-> "NH2" Residue "N GLU 221": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "R GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.70, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.5 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: 1.21 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: 2.68 Time building geometry restraints manager: 3.80 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: 99.20 - 106.18: 202 106.18 - 113.16: 4785 113.16 - 120.14: 3219 120.14 - 127.12: 3822 127.12 - 134.10: 110 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 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.215 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.229 2.440 nonbonded pdb=" NH1 ARG A 93 " pdb=" OD1 ASP A 124 " model vdw 2.279 2.520 nonbonded pdb=" O THR B 47 " pdb=" OG1 THR B 47 " model vdw 2.286 2.440 ... (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 ========== 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: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.950 Find NCS groups from input model: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- 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 8936 Z= 0.316 Angle : 0.808 12.674 12138 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 0.940 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: 0.1939 time to fit residues: 60.8257 Evaluate side-chains 172 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8936 Z= 0.275 Angle : 0.679 13.958 12138 Z= 0.344 Chirality : 0.045 0.172 1368 Planarity : 0.005 0.053 1555 Dihedral : 5.115 45.680 1312 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.24 % Allowed : 22.27 % Favored : 72.49 % 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: 0.49 (0.26), residues: 1120 helix: 1.45 (0.28), residues: 358 sheet: -0.48 (0.32), residues: 262 loop : 0.10 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 297 HIS 0.006 0.001 HIS B 62 PHE 0.034 0.003 PHE B 199 TYR 0.020 0.002 TYR B 59 ARG 0.006 0.001 ARG B 219 *********************** 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 230 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.6071 (ptt) REVERT: A 53 MET cc_start: 0.7359 (tmm) cc_final: 0.7006 (tmm) REVERT: B 176 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: B 212 ASP cc_start: 0.7199 (t0) cc_final: 0.6901 (t0) REVERT: B 234 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: N 71 SER cc_start: 0.7887 (p) cc_final: 0.7557 (m) REVERT: N 76 LYS cc_start: 0.7236 (mtpp) cc_final: 0.7030 (mppt) REVERT: N 141 MET cc_start: 0.7195 (tpp) cc_final: 0.6969 (tpp) REVERT: R 20 PHE cc_start: 0.7906 (t80) cc_final: 0.7695 (t80) REVERT: R 28 ARG cc_start: 0.8173 (tmt-80) cc_final: 0.7561 (mmm160) REVERT: R 209 LEU cc_start: 0.7110 (mt) cc_final: 0.6769 (mt) outliers start: 48 outliers final: 19 residues processed: 215 average time/residue: 0.1675 time to fit residues: 52.1634 Evaluate side-chains 176 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 176 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP 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 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 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 223 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8936 Z= 0.230 Angle : 0.616 9.884 12138 Z= 0.309 Chirality : 0.043 0.219 1368 Planarity : 0.004 0.047 1555 Dihedral : 4.904 39.950 1312 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.15 % Allowed : 24.34 % Favored : 71.51 % 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: 0.68 (0.26), residues: 1120 helix: 1.73 (0.28), residues: 365 sheet: -0.44 (0.30), residues: 273 loop : 0.14 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.016 0.002 HIS N 168 PHE 0.019 0.002 PHE B 199 TYR 0.016 0.001 TYR B 59 ARG 0.003 0.000 ARG B 52 *********************** 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 211 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 0.926 Fit side-chains REVERT: A 53 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6824 (tmm) REVERT: A 196 GLU cc_start: 0.7048 (tt0) cc_final: 0.6790 (tt0) REVERT: B 66 ASP cc_start: 0.7487 (t0) cc_final: 0.7174 (t0) REVERT: B 124 TYR cc_start: 0.8584 (m-80) cc_final: 0.7880 (m-80) REVERT: B 170 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: B 212 ASP cc_start: 0.7322 (t0) cc_final: 0.7009 (t0) REVERT: B 217 MET cc_start: 0.7497 (ptp) cc_final: 0.7137 (ptt) REVERT: N 39 GLN cc_start: 0.6228 (tt0) cc_final: 0.5906 (tt0) REVERT: N 60 TYR cc_start: 0.7217 (m-80) cc_final: 0.6908 (m-80) REVERT: N 71 SER cc_start: 0.8181 (p) cc_final: 0.7969 (m) REVERT: N 76 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7259 (mppt) REVERT: N 83 MET cc_start: 0.6451 (mmm) cc_final: 0.6180 (mmt) REVERT: R 35 ARG cc_start: 0.6363 (mmm160) cc_final: 0.5620 (mmp-170) REVERT: R 184 PHE cc_start: 0.6956 (t80) cc_final: 0.6700 (t80) outliers start: 38 outliers final: 21 residues processed: 196 average time/residue: 0.2084 time to fit residues: 55.7998 Evaluate side-chains 178 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 183 ASP 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 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR 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 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 239 THR 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 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 40.0000 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** B 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8936 Z= 0.215 Angle : 0.591 11.249 12138 Z= 0.295 Chirality : 0.042 0.175 1368 Planarity : 0.004 0.039 1555 Dihedral : 4.740 40.602 1312 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.82 % Allowed : 25.00 % Favored : 71.18 % 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: 0.82 (0.26), residues: 1120 helix: 1.99 (0.28), residues: 361 sheet: -0.36 (0.31), residues: 280 loop : 0.11 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.010 0.001 HIS B 311 PHE 0.019 0.002 PHE B 199 TYR 0.018 0.001 TYR N 191 ARG 0.005 0.000 ARG A 35 *********************** 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 206 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6797 (tmt) REVERT: B 66 ASP cc_start: 0.7640 (t0) cc_final: 0.7429 (t0) REVERT: B 170 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: B 212 ASP cc_start: 0.7222 (t0) cc_final: 0.6908 (t0) REVERT: B 260 GLU cc_start: 0.8018 (tt0) cc_final: 0.7699 (tt0) REVERT: G 47 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7191 (mt-10) REVERT: N 39 GLN cc_start: 0.7117 (tt0) cc_final: 0.6894 (tt0) REVERT: N 76 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7422 (mppt) REVERT: N 83 MET cc_start: 0.7237 (mmm) cc_final: 0.6964 (mmm) REVERT: N 232 GLN cc_start: 0.7945 (pp30) cc_final: 0.7017 (pm20) REVERT: R 35 ARG cc_start: 0.6495 (mmm160) cc_final: 0.5647 (mmp-170) REVERT: R 97 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7876 (mt) REVERT: R 184 PHE cc_start: 0.7142 (t80) cc_final: 0.6854 (t80) REVERT: R 217 ARG cc_start: 0.6600 (mtm180) cc_final: 0.6396 (mtm180) outliers start: 35 outliers final: 22 residues processed: 199 average time/residue: 0.2062 time to fit residues: 55.9008 Evaluate side-chains 179 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 139 VAL 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 B residue 74 SER 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 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL 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 1 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 223 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8936 Z= 0.215 Angle : 0.584 11.221 12138 Z= 0.292 Chirality : 0.042 0.162 1368 Planarity : 0.004 0.040 1555 Dihedral : 4.752 41.567 1312 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.88 (0.26), residues: 1120 helix: 2.12 (0.28), residues: 359 sheet: -0.33 (0.31), residues: 277 loop : 0.08 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS R 216 PHE 0.019 0.002 PHE R 16 TYR 0.022 0.001 TYR N 191 ARG 0.005 0.000 ARG N 38 *********************** 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 204 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6764 (tmt) REVERT: B 74 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8616 (p) REVERT: B 170 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: B 212 ASP cc_start: 0.7261 (t0) cc_final: 0.6888 (t0) REVERT: B 311 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8080 (t-90) REVERT: B 322 ASP cc_start: 0.7840 (t0) cc_final: 0.7631 (t0) REVERT: N 76 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7391 (mppt) REVERT: R 28 ARG cc_start: 0.8175 (tmt-80) cc_final: 0.6635 (mmt180) REVERT: R 35 ARG cc_start: 0.6530 (mmm160) cc_final: 0.5626 (mmp-170) REVERT: R 97 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8033 (mt) outliers start: 38 outliers final: 21 residues processed: 197 average time/residue: 0.2178 time to fit residues: 57.8210 Evaluate side-chains 176 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 74 SER 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 233 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 197 ILE 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 62 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 259 GLN N 168 HIS N 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8936 Z= 0.280 Angle : 0.627 13.079 12138 Z= 0.311 Chirality : 0.044 0.246 1368 Planarity : 0.004 0.033 1555 Dihedral : 4.947 47.731 1312 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.13 % Allowed : 24.78 % Favored : 70.09 % 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: 0.80 (0.26), residues: 1120 helix: 2.03 (0.28), residues: 360 sheet: -0.31 (0.32), residues: 263 loop : -0.00 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 131 HIS 0.004 0.001 HIS R 216 PHE 0.019 0.002 PHE N 213 TYR 0.020 0.002 TYR N 191 ARG 0.006 0.000 ARG N 38 *********************** 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 215 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6800 (tmt) REVERT: B 153 ASP cc_start: 0.7348 (m-30) cc_final: 0.6968 (m-30) REVERT: B 170 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: B 212 ASP cc_start: 0.7263 (t0) cc_final: 0.6919 (t0) REVERT: B 217 MET cc_start: 0.7508 (ptp) cc_final: 0.7193 (ptt) REVERT: B 234 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 246 ASP cc_start: 0.7872 (t0) cc_final: 0.7580 (m-30) REVERT: B 259 GLN cc_start: 0.7820 (pt0) cc_final: 0.7208 (pt0) REVERT: B 266 HIS cc_start: 0.8289 (t-90) cc_final: 0.8001 (t-90) REVERT: B 311 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8008 (t-90) REVERT: N 76 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7619 (mppt) REVERT: N 232 GLN cc_start: 0.7947 (pp30) cc_final: 0.7272 (pp30) REVERT: R 9 PHE cc_start: 0.8378 (t80) cc_final: 0.8099 (t80) REVERT: R 35 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6248 (ptp-170) REVERT: R 97 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8130 (mt) outliers start: 47 outliers final: 34 residues processed: 202 average time/residue: 0.2083 time to fit residues: 57.6819 Evaluate side-chains 204 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU 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 198 VAL Chi-restraints excluded: chain A residue 223 ASN 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 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 234 PHE 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 316 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 22 CYS 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 R residue 97 LEU Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 257 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN N 39 GLN N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.195 Angle : 0.580 12.043 12138 Z= 0.284 Chirality : 0.042 0.165 1368 Planarity : 0.003 0.032 1555 Dihedral : 4.775 49.690 1312 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.37 % Allowed : 25.55 % Favored : 70.09 % 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: 0.92 (0.26), residues: 1120 helix: 2.13 (0.28), residues: 360 sheet: -0.21 (0.31), residues: 263 loop : 0.05 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 PHE 0.015 0.001 PHE B 199 TYR 0.021 0.001 TYR N 191 ARG 0.005 0.000 ARG N 38 *********************** 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 204 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 53 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6749 (tmt) REVERT: A 151 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: A 244 ASN cc_start: 0.8453 (m-40) cc_final: 0.8186 (t0) REVERT: B 74 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 153 ASP cc_start: 0.7351 (m-30) cc_final: 0.6948 (m-30) REVERT: B 170 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 212 ASP cc_start: 0.7162 (t0) cc_final: 0.6921 (t0) REVERT: B 219 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7213 (ttm-80) REVERT: B 246 ASP cc_start: 0.7859 (t0) cc_final: 0.7573 (m-30) REVERT: B 259 GLN cc_start: 0.7777 (pt0) cc_final: 0.7142 (pt0) REVERT: B 311 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8049 (t-90) REVERT: G 42 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: G 58 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7539 (tm-30) REVERT: N 76 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7628 (mppt) REVERT: N 87 ARG cc_start: 0.6149 (ptp90) cc_final: 0.4867 (ptp90) REVERT: R 9 PHE cc_start: 0.8415 (t80) cc_final: 0.8133 (t80) REVERT: R 28 ARG cc_start: 0.8175 (tmt-80) cc_final: 0.6680 (mmt180) REVERT: R 35 ARG cc_start: 0.6758 (mmm160) cc_final: 0.5855 (mmp-170) REVERT: R 250 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6785 (t80) outliers start: 40 outliers final: 22 residues processed: 192 average time/residue: 0.2021 time to fit residues: 53.3407 Evaluate side-chains 188 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 122 LEU 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 223 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL 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 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 42 GLU 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 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 276 THR 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 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN N 39 GLN N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8936 Z= 0.203 Angle : 0.598 13.839 12138 Z= 0.289 Chirality : 0.042 0.157 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.769 51.544 1312 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.37 % Allowed : 26.09 % Favored : 69.54 % 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: 0.95 (0.26), residues: 1120 helix: 2.20 (0.28), residues: 360 sheet: -0.17 (0.32), residues: 263 loop : 0.01 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS R 216 PHE 0.015 0.001 PHE B 199 TYR 0.018 0.001 TYR N 191 ARG 0.004 0.000 ARG B 52 *********************** 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 205 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 53 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6712 (tmt) REVERT: A 151 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: A 244 ASN cc_start: 0.8455 (m-40) cc_final: 0.8245 (t0) REVERT: B 153 ASP cc_start: 0.7307 (m-30) cc_final: 0.6926 (m-30) REVERT: B 170 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: B 219 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7286 (ttm-80) REVERT: B 246 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: B 259 GLN cc_start: 0.7781 (pt0) cc_final: 0.7139 (pt0) REVERT: B 311 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: G 42 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: N 76 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7654 (mppt) REVERT: R 9 PHE cc_start: 0.8474 (t80) cc_final: 0.8172 (t80) REVERT: R 28 ARG cc_start: 0.8174 (tmt-80) cc_final: 0.6655 (mmt180) REVERT: R 35 ARG cc_start: 0.6780 (mmm160) cc_final: 0.5891 (mmp-170) outliers start: 40 outliers final: 27 residues processed: 194 average time/residue: 0.2055 time to fit residues: 55.4280 Evaluate side-chains 193 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU 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 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 135 VAL 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 190 LEU Chi-restraints excluded: chain B residue 246 ASP 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 323 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 22 CYS 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 R residue 42 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 276 THR 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 102 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 168 HIS R 47 ASN R 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.8415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8936 Z= 0.176 Angle : 0.581 13.157 12138 Z= 0.281 Chirality : 0.041 0.147 1368 Planarity : 0.003 0.033 1555 Dihedral : 4.690 52.516 1312 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.60 % Allowed : 27.07 % Favored : 69.32 % 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: 1.06 (0.26), residues: 1120 helix: 2.30 (0.28), residues: 360 sheet: -0.13 (0.32), residues: 263 loop : 0.07 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.003 0.001 HIS N 35 PHE 0.015 0.001 PHE B 199 TYR 0.019 0.001 TYR N 191 ARG 0.004 0.000 ARG B 52 *********************** 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 196 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 53 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6649 (tmt) REVERT: A 151 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: B 153 ASP cc_start: 0.7313 (m-30) cc_final: 0.6921 (m-30) REVERT: B 170 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 219 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7302 (ttm-80) REVERT: B 246 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: B 311 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7985 (t-90) REVERT: G 42 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: N 5 VAL cc_start: 0.7821 (t) cc_final: 0.7597 (p) REVERT: N 76 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7669 (mppt) REVERT: R 9 PHE cc_start: 0.8578 (t80) cc_final: 0.8264 (t80) REVERT: R 28 ARG cc_start: 0.8150 (tmt-80) cc_final: 0.6638 (mmt180) REVERT: R 35 ARG cc_start: 0.6770 (mmm160) cc_final: 0.5896 (mmp-170) outliers start: 33 outliers final: 23 residues processed: 185 average time/residue: 0.2178 time to fit residues: 54.3227 Evaluate side-chains 183 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU 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 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL 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 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 42 GLU 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 R residue 42 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 39 GLN N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.8543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.166 Angle : 0.583 12.859 12138 Z= 0.284 Chirality : 0.041 0.168 1368 Planarity : 0.003 0.032 1555 Dihedral : 4.600 52.808 1312 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.93 % Allowed : 27.18 % Favored : 68.89 % 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: 1.07 (0.26), residues: 1120 helix: 2.31 (0.28), residues: 360 sheet: -0.13 (0.32), residues: 265 loop : 0.09 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.004 0.001 HIS N 35 PHE 0.026 0.001 PHE R 16 TYR 0.018 0.001 TYR N 191 ARG 0.004 0.000 ARG B 52 ********************** 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 198 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 53 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6600 (tmt) REVERT: A 83 MET cc_start: 0.7699 (ttm) cc_final: 0.7478 (ttm) REVERT: A 151 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 212 TYR cc_start: 0.8599 (m-80) cc_final: 0.8337 (m-10) REVERT: A 230 ASP cc_start: 0.8093 (m-30) cc_final: 0.7892 (m-30) REVERT: B 153 ASP cc_start: 0.7314 (m-30) cc_final: 0.6929 (m-30) REVERT: B 170 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 219 ARG cc_start: 0.7581 (tpp80) cc_final: 0.7298 (ttm-80) REVERT: B 246 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: B 311 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7927 (t-90) REVERT: G 42 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: N 5 VAL cc_start: 0.7886 (t) cc_final: 0.7674 (p) REVERT: N 76 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7640 (mppt) REVERT: R 9 PHE cc_start: 0.8660 (t80) cc_final: 0.8351 (t80) REVERT: R 28 ARG cc_start: 0.8127 (tmt-80) cc_final: 0.6607 (mmt180) REVERT: R 35 ARG cc_start: 0.6766 (mmm160) cc_final: 0.5930 (mmp-170) outliers start: 36 outliers final: 28 residues processed: 187 average time/residue: 0.2144 time to fit residues: 54.5072 Evaluate side-chains 189 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL 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 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 246 ASP 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 323 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 173 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN A 244 ASN B 259 GLN N 39 GLN ** N 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.171039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117925 restraints weight = 10595.542| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.36 r_work: 0.3253 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8936 Z= 0.221 Angle : 0.607 12.689 12138 Z= 0.296 Chirality : 0.043 0.193 1368 Planarity : 0.003 0.031 1555 Dihedral : 4.772 57.588 1312 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.71 % Allowed : 27.62 % Favored : 68.67 % 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: 2.23 (0.28), residues: 360 sheet: -0.20 (0.32), residues: 265 loop : 0.10 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS R 137 PHE 0.015 0.001 PHE B 199 TYR 0.019 0.001 TYR B 59 ARG 0.007 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.75 seconds wall clock time: 40 minutes 14.65 seconds (2414.65 seconds total)