Starting phenix.real_space_refine on Wed Sep 17 11:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.map" model { file = "/net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixj_60971/09_2025/9ixj_60971.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 5106 2.51 5 N 1404 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8055 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1868 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 4 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2604 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2150 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8055 At special positions: 0 Unit cell: (82.5, 103.4, 133.1, 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 1493 8.00 N 1404 7.00 C 5106 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=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 174 " 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: 0.65 Conformation dependent library (CDL) restraints added in 419.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 40.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.800A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.523A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.698A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 4.000A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.801A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.230A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.560A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 removed outlier: 3.718A pdb=" N GLN A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 395 " --> pdb=" O HIS A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.785A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.851A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.671A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.572A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.873A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 46 removed outlier: 3.741A pdb=" N ASN R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 54 through 71 Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.536A pdb=" N SER R 75 " --> pdb=" O VAL R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 122 Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 131 through 155 removed outlier: 4.403A pdb=" N SER R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 217 removed outlier: 3.777A pdb=" N ARG R 215 " --> pdb=" O ASP R 211 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE R 216 " --> pdb=" O GLN R 212 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 261 removed outlier: 3.531A pdb=" N THR R 235 " --> pdb=" O LYS R 231 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 244 " --> pdb=" O MET R 240 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 262 through 265 removed outlier: 3.808A pdb=" N ILE R 265 " --> pdb=" O ASP R 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 262 through 265' Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 290 removed outlier: 3.883A pdb=" N LEU R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.759A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.759A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 43 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.955A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.094A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.082A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.759A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.374A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.176A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.87 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: 2645 1.34 - 1.46: 1896 1.46 - 1.58: 3597 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8209 Sorted by residual: bond pdb=" CB HSM R 401 " pdb=" CG HSM R 401 " ideal model delta sigma weight residual 1.496 1.460 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CE1 HSM R 401 " pdb=" NE2 HSM R 401 " ideal model delta sigma weight residual 1.354 1.383 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C CYS R 102 " pdb=" O CYS R 102 " ideal model delta sigma weight residual 1.236 1.249 -0.012 1.15e-02 7.56e+03 1.17e+00 bond pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" C ILE R 106 " pdb=" O ILE R 106 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.17e-02 7.31e+03 8.68e-01 ... (remaining 8204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 10904 1.94 - 3.87: 205 3.87 - 5.81: 19 5.81 - 7.75: 5 7.75 - 9.68: 2 Bond angle restraints: 11135 Sorted by residual: angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.24 117.12 5.12 1.57e+00 4.06e-01 1.06e+01 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" C PHE B 234 " ideal model delta sigma weight residual 110.48 114.80 -4.32 1.48e+00 4.57e-01 8.52e+00 angle pdb=" C SER A 349 " pdb=" N THR A 350 " pdb=" CA THR A 350 " ideal model delta sigma weight residual 122.83 118.52 4.31 1.54e+00 4.22e-01 7.85e+00 angle pdb=" CA LEU R 70 " pdb=" CB LEU R 70 " pdb=" CG LEU R 70 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 110.44 113.67 -3.23 1.20e+00 6.94e-01 7.26e+00 ... (remaining 11130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4506 17.85 - 35.69: 361 35.69 - 53.54: 46 53.54 - 71.39: 15 71.39 - 89.23: 12 Dihedral angle restraints: 4940 sinusoidal: 1950 harmonic: 2990 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE R 191 " pdb=" C PHE R 191 " pdb=" N TYR R 192 " pdb=" CA TYR R 192 " ideal model delta harmonic sigma weight residual 180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1099 0.065 - 0.129: 166 0.129 - 0.194: 13 0.194 - 0.258: 2 0.258 - 0.323: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 2.79 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.66 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1278 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 332 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 236 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO G 49 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.028 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 330 2.72 - 3.27: 7327 3.27 - 3.81: 11829 3.81 - 4.36: 13677 4.36 - 4.90: 25568 Nonbonded interactions: 58731 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.178 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.216 3.040 nonbonded pdb=" OG SER N 7 " pdb=" OG SER N 21 " model vdw 2.264 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.301 3.040 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.337 3.120 ... (remaining 58726 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=1.00 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: 1.100 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.004 0.036 8212 Z= 0.201 Angle : 0.660 9.681 11141 Z= 0.381 Chirality : 0.048 0.323 1281 Planarity : 0.005 0.071 1412 Dihedral : 13.871 89.233 2995 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.26), residues: 1009 helix: 2.57 (0.28), residues: 354 sheet: 0.42 (0.35), residues: 220 loop : -1.73 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.020 0.002 TYR R 202 PHE 0.035 0.002 PHE B 234 TRP 0.030 0.002 TRP B 82 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8209) covalent geometry : angle 0.65983 (11135) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.21883 ( 6) hydrogen bonds : bond 0.12929 ( 393) hydrogen bonds : angle 5.38316 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.312 Fit side-chains REVERT: B 55 LEU cc_start: 0.8377 (mp) cc_final: 0.8109 (mt) REVERT: B 79 LEU cc_start: 0.8381 (tp) cc_final: 0.7902 (tp) REVERT: B 333 ASP cc_start: 0.7328 (p0) cc_final: 0.6990 (p0) REVERT: G 21 MET cc_start: 0.7540 (tpp) cc_final: 0.7231 (tpp) REVERT: G 42 GLU cc_start: 0.7076 (tp30) cc_final: 0.6823 (tp30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.7423 time to fit residues: 113.5411 Evaluate side-chains 128 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 156 GLN B 176 GLN N 31 ASN N 74 ASN R 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106175 restraints weight = 11560.223| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.34 r_work: 0.3239 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8212 Z= 0.169 Angle : 0.563 10.440 11141 Z= 0.309 Chirality : 0.044 0.144 1281 Planarity : 0.005 0.066 1412 Dihedral : 4.719 23.846 1186 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.04 % Allowed : 8.34 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.27), residues: 1009 helix: 2.66 (0.28), residues: 363 sheet: 0.58 (0.36), residues: 212 loop : -1.65 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.015 0.001 TYR R 94 PHE 0.018 0.002 PHE R 206 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8209) covalent geometry : angle 0.56266 (11135) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.16548 ( 6) hydrogen bonds : bond 0.07155 ( 393) hydrogen bonds : angle 4.52164 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.308 Fit side-chains REVERT: B 52 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8216 (ptp90) REVERT: B 55 LEU cc_start: 0.8527 (mp) cc_final: 0.8205 (mt) REVERT: B 304 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7453 (ttt180) REVERT: B 333 ASP cc_start: 0.7615 (p0) cc_final: 0.7341 (p0) REVERT: G 21 MET cc_start: 0.7714 (tpp) cc_final: 0.7387 (tpp) REVERT: G 42 GLU cc_start: 0.7756 (tp30) cc_final: 0.7522 (tp30) outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.6788 time to fit residues: 90.6735 Evaluate side-chains 130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 67 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 0.0060 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109431 restraints weight = 11569.331| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.35 r_work: 0.3285 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8212 Z= 0.112 Angle : 0.495 10.814 11141 Z= 0.269 Chirality : 0.042 0.139 1281 Planarity : 0.004 0.061 1412 Dihedral : 4.227 22.507 1186 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.97 % Allowed : 9.04 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 1009 helix: 2.98 (0.27), residues: 363 sheet: 0.69 (0.35), residues: 212 loop : -1.54 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.013 0.001 TYR R 94 PHE 0.014 0.001 PHE R 206 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8209) covalent geometry : angle 0.49464 (11135) SS BOND : bond 0.00329 ( 3) SS BOND : angle 0.76715 ( 6) hydrogen bonds : bond 0.05415 ( 393) hydrogen bonds : angle 4.17572 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.313 Fit side-chains REVERT: A 356 ARG cc_start: 0.8221 (mtp180) cc_final: 0.8018 (mtp180) REVERT: B 52 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8207 (ptp90) REVERT: B 79 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8183 (tp) REVERT: B 234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: B 304 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7529 (ttt180) REVERT: B 314 ARG cc_start: 0.8421 (ttt180) cc_final: 0.8131 (ttt180) REVERT: B 333 ASP cc_start: 0.7479 (p0) cc_final: 0.7202 (p0) REVERT: G 21 MET cc_start: 0.7674 (tpp) cc_final: 0.7383 (tpp) REVERT: G 42 GLU cc_start: 0.7774 (tp30) cc_final: 0.7547 (tp30) REVERT: R 125 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7942 (mtt180) outliers start: 17 outliers final: 4 residues processed: 135 average time/residue: 0.7373 time to fit residues: 104.2119 Evaluate side-chains 130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.3980 chunk 72 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.0050 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109624 restraints weight = 11767.496| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.38 r_work: 0.3276 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8212 Z= 0.110 Angle : 0.481 10.542 11141 Z= 0.262 Chirality : 0.042 0.135 1281 Planarity : 0.004 0.058 1412 Dihedral : 4.055 21.986 1186 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.74 % Allowed : 10.66 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1009 helix: 3.08 (0.27), residues: 365 sheet: 0.69 (0.35), residues: 218 loop : -1.47 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.012 0.001 TYR R 94 PHE 0.024 0.002 PHE N 108 TRP 0.014 0.001 TRP B 99 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8209) covalent geometry : angle 0.48106 (11135) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.80083 ( 6) hydrogen bonds : bond 0.05192 ( 393) hydrogen bonds : angle 4.06092 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.266 Fit side-chains REVERT: B 52 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (ptp90) REVERT: B 79 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 155 ASN cc_start: 0.8375 (t0) cc_final: 0.7859 (t0) REVERT: B 217 MET cc_start: 0.8242 (pmm) cc_final: 0.7958 (pmm) REVERT: B 234 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: B 304 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7656 (ttt180) REVERT: B 333 ASP cc_start: 0.7430 (p0) cc_final: 0.7206 (p0) REVERT: G 21 MET cc_start: 0.7749 (tpp) cc_final: 0.7458 (tpp) REVERT: G 42 GLU cc_start: 0.7801 (tp30) cc_final: 0.7583 (tp30) REVERT: N 17 SER cc_start: 0.8752 (p) cc_final: 0.8271 (m) outliers start: 15 outliers final: 7 residues processed: 134 average time/residue: 0.6563 time to fit residues: 92.5115 Evaluate side-chains 137 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107835 restraints weight = 11613.377| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.37 r_work: 0.3241 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8212 Z= 0.145 Angle : 0.516 10.204 11141 Z= 0.283 Chirality : 0.043 0.139 1281 Planarity : 0.004 0.055 1412 Dihedral : 4.162 21.658 1186 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.32 % Allowed : 11.01 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1009 helix: 3.00 (0.27), residues: 367 sheet: 0.73 (0.35), residues: 218 loop : -1.44 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.016 0.001 TYR R 94 PHE 0.031 0.002 PHE A 222 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8209) covalent geometry : angle 0.51601 (11135) SS BOND : bond 0.00476 ( 3) SS BOND : angle 0.89734 ( 6) hydrogen bonds : bond 0.06217 ( 393) hydrogen bonds : angle 4.15720 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.323 Fit side-chains REVERT: B 52 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8192 (ptp90) REVERT: B 79 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 155 ASN cc_start: 0.8414 (t0) cc_final: 0.8193 (t0) REVERT: B 234 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 304 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7706 (ttt180) REVERT: B 333 ASP cc_start: 0.7522 (p0) cc_final: 0.7290 (p0) REVERT: G 21 MET cc_start: 0.7733 (tpp) cc_final: 0.7451 (tpp) REVERT: G 42 GLU cc_start: 0.7784 (tp30) cc_final: 0.7562 (tp30) REVERT: N 17 SER cc_start: 0.8742 (p) cc_final: 0.8269 (m) REVERT: R 125 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7961 (mtt180) outliers start: 20 outliers final: 9 residues processed: 138 average time/residue: 0.7360 time to fit residues: 106.4169 Evaluate side-chains 140 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106882 restraints weight = 11581.233| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.36 r_work: 0.3219 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8212 Z= 0.168 Angle : 0.546 10.251 11141 Z= 0.299 Chirality : 0.043 0.143 1281 Planarity : 0.004 0.055 1412 Dihedral : 4.288 21.172 1186 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.20 % Allowed : 11.24 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.27), residues: 1009 helix: 2.91 (0.27), residues: 367 sheet: 0.77 (0.35), residues: 217 loop : -1.45 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 210 TYR 0.017 0.002 TYR R 94 PHE 0.035 0.002 PHE A 222 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8209) covalent geometry : angle 0.54542 (11135) SS BOND : bond 0.00529 ( 3) SS BOND : angle 0.98523 ( 6) hydrogen bonds : bond 0.06882 ( 393) hydrogen bonds : angle 4.25746 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.328 Fit side-chains REVERT: B 52 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8217 (ptp90) REVERT: B 79 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8196 (tp) REVERT: B 234 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: B 304 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7807 (ttt180) REVERT: B 333 ASP cc_start: 0.7585 (p0) cc_final: 0.7303 (p0) REVERT: G 21 MET cc_start: 0.7737 (tpp) cc_final: 0.7425 (tpp) REVERT: G 42 GLU cc_start: 0.7787 (tp30) cc_final: 0.7563 (tp30) REVERT: N 17 SER cc_start: 0.8746 (p) cc_final: 0.8279 (m) REVERT: N 63 SER cc_start: 0.8608 (t) cc_final: 0.8241 (m) REVERT: R 118 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7676 (m) REVERT: R 125 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.8018 (mtt180) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.7627 time to fit residues: 107.2460 Evaluate side-chains 142 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107692 restraints weight = 11617.236| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.39 r_work: 0.3235 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8212 Z= 0.146 Angle : 0.522 10.173 11141 Z= 0.288 Chirality : 0.043 0.139 1281 Planarity : 0.004 0.054 1412 Dihedral : 4.197 20.738 1186 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 12.05 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1009 helix: 2.98 (0.27), residues: 367 sheet: 0.77 (0.35), residues: 217 loop : -1.43 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 210 TYR 0.015 0.001 TYR N 60 PHE 0.030 0.002 PHE A 222 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8209) covalent geometry : angle 0.52187 (11135) SS BOND : bond 0.00465 ( 3) SS BOND : angle 0.95745 ( 6) hydrogen bonds : bond 0.06356 ( 393) hydrogen bonds : angle 4.18117 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.332 Fit side-chains REVERT: B 52 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8200 (ptp90) REVERT: B 79 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: B 304 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7800 (ttt180) REVERT: B 333 ASP cc_start: 0.7584 (p0) cc_final: 0.7295 (p0) REVERT: G 21 MET cc_start: 0.7755 (tpp) cc_final: 0.7440 (tpp) REVERT: G 42 GLU cc_start: 0.7812 (tp30) cc_final: 0.7605 (tp30) REVERT: N 17 SER cc_start: 0.8739 (p) cc_final: 0.8268 (m) REVERT: N 63 SER cc_start: 0.8604 (t) cc_final: 0.8227 (m) REVERT: R 125 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7975 (mtt180) outliers start: 19 outliers final: 14 residues processed: 138 average time/residue: 0.7462 time to fit residues: 107.9115 Evaluate side-chains 147 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 156 GLN N 31 ASN N 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107345 restraints weight = 11627.206| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.33 r_work: 0.3229 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8212 Z= 0.167 Angle : 0.541 10.183 11141 Z= 0.298 Chirality : 0.043 0.143 1281 Planarity : 0.004 0.053 1412 Dihedral : 4.256 20.716 1186 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 12.17 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.27), residues: 1009 helix: 2.92 (0.27), residues: 367 sheet: 0.76 (0.35), residues: 217 loop : -1.46 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 210 TYR 0.016 0.002 TYR R 94 PHE 0.028 0.002 PHE A 222 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8209) covalent geometry : angle 0.54043 (11135) SS BOND : bond 0.00533 ( 3) SS BOND : angle 1.03632 ( 6) hydrogen bonds : bond 0.06772 ( 393) hydrogen bonds : angle 4.21944 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.208 Fit side-chains REVERT: B 52 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8206 (ptp90) REVERT: B 79 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 217 MET cc_start: 0.8258 (pmm) cc_final: 0.7987 (pmm) REVERT: B 234 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: B 304 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: B 333 ASP cc_start: 0.7616 (p0) cc_final: 0.7326 (p0) REVERT: G 21 MET cc_start: 0.7741 (tpp) cc_final: 0.7429 (tpp) REVERT: G 42 GLU cc_start: 0.7718 (tp30) cc_final: 0.7500 (tp30) REVERT: N 17 SER cc_start: 0.8727 (p) cc_final: 0.8261 (m) REVERT: N 63 SER cc_start: 0.8607 (t) cc_final: 0.8231 (m) REVERT: R 118 CYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7673 (m) REVERT: R 125 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.8037 (mtt180) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.7287 time to fit residues: 103.6774 Evaluate side-chains 146 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107710 restraints weight = 11607.204| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.33 r_work: 0.3235 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8212 Z= 0.155 Angle : 0.528 10.106 11141 Z= 0.291 Chirality : 0.043 0.140 1281 Planarity : 0.004 0.053 1412 Dihedral : 4.213 20.446 1186 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.67 % Allowed : 12.28 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.27), residues: 1009 helix: 2.95 (0.27), residues: 367 sheet: 0.74 (0.35), residues: 217 loop : -1.44 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 210 TYR 0.015 0.001 TYR N 60 PHE 0.025 0.002 PHE A 222 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8209) covalent geometry : angle 0.52721 (11135) SS BOND : bond 0.00486 ( 3) SS BOND : angle 1.03988 ( 6) hydrogen bonds : bond 0.06509 ( 393) hydrogen bonds : angle 4.18232 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.326 Fit side-chains REVERT: B 52 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8202 (ptp90) REVERT: B 79 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 217 MET cc_start: 0.8249 (pmm) cc_final: 0.7977 (pmm) REVERT: B 234 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: B 304 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7838 (ttt180) REVERT: B 333 ASP cc_start: 0.7606 (p0) cc_final: 0.7322 (p0) REVERT: G 21 MET cc_start: 0.7729 (tpp) cc_final: 0.7407 (tpp) REVERT: G 42 GLU cc_start: 0.7764 (tp30) cc_final: 0.7563 (tp30) REVERT: N 17 SER cc_start: 0.8719 (p) cc_final: 0.8250 (m) REVERT: N 63 SER cc_start: 0.8616 (t) cc_final: 0.8240 (m) REVERT: R 125 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8029 (mtt180) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.7371 time to fit residues: 105.7529 Evaluate side-chains 145 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 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 155 ASN B 176 GLN N 31 ASN N 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107947 restraints weight = 11583.073| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.33 r_work: 0.3230 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8212 Z= 0.146 Angle : 0.527 10.155 11141 Z= 0.288 Chirality : 0.043 0.140 1281 Planarity : 0.004 0.053 1412 Dihedral : 4.173 20.419 1186 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.09 % Allowed : 13.33 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.27), residues: 1009 helix: 2.97 (0.27), residues: 367 sheet: 0.79 (0.35), residues: 217 loop : -1.41 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 210 TYR 0.015 0.001 TYR N 60 PHE 0.024 0.002 PHE A 222 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8209) covalent geometry : angle 0.52691 (11135) SS BOND : bond 0.00467 ( 3) SS BOND : angle 1.01164 ( 6) hydrogen bonds : bond 0.06356 ( 393) hydrogen bonds : angle 4.14053 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.268 Fit side-chains REVERT: B 52 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8207 (ptp90) REVERT: B 61 MET cc_start: 0.8260 (tmm) cc_final: 0.8004 (tmm) REVERT: B 79 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 217 MET cc_start: 0.8247 (pmm) cc_final: 0.7983 (pmm) REVERT: B 234 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: B 304 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7857 (ttt180) REVERT: B 333 ASP cc_start: 0.7597 (p0) cc_final: 0.7305 (p0) REVERT: G 21 MET cc_start: 0.7736 (tpp) cc_final: 0.7442 (tpp) REVERT: G 42 GLU cc_start: 0.7740 (tp30) cc_final: 0.7536 (tp30) REVERT: N 17 SER cc_start: 0.8710 (p) cc_final: 0.8239 (m) REVERT: R 283 LEU cc_start: 0.8152 (mp) cc_final: 0.7944 (mt) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.7522 time to fit residues: 109.9681 Evaluate side-chains 147 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 118 CYS Chi-restraints excluded: chain R residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 31 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107820 restraints weight = 11563.266| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.33 r_work: 0.3236 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8212 Z= 0.152 Angle : 0.531 10.141 11141 Z= 0.291 Chirality : 0.043 0.141 1281 Planarity : 0.004 0.053 1412 Dihedral : 4.187 20.351 1186 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 13.44 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.27), residues: 1009 helix: 2.95 (0.27), residues: 367 sheet: 0.81 (0.35), residues: 217 loop : -1.43 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 210 TYR 0.015 0.001 TYR R 94 PHE 0.025 0.002 PHE A 222 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8209) covalent geometry : angle 0.53048 (11135) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.99929 ( 6) hydrogen bonds : bond 0.06471 ( 393) hydrogen bonds : angle 4.14764 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3161.51 seconds wall clock time: 54 minutes 30.12 seconds (3270.12 seconds total)