Starting phenix.real_space_refine on Wed Mar 4 18:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jjo_22357/03_2026/7jjo_22357.map" } resolution = 2.6 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= 1.248 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 5011 2.51 5 N 1379 2.21 5 O 1451 1.98 5 H 7749 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15641 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3310 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 882 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 4419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4419 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.18 Number of scatterers: 15641 At special positions: 0 Unit cell: (81.396, 100.016, 138.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 1451 8.00 N 1379 7.00 C 5011 6.00 H 7749 1.00 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 114 " - pdb=" SG CYS R 199 " 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: 1.32 Conformation dependent library (CDL) restraints added in 434.4 milliseconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.2% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.607A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.582A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.688A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.834A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.539A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 288 removed outlier: 4.059A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.611A pdb=" N ALA A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 354 through 377 Processing helix chain 'G' and resid 9 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 70 through 73 Processing helix chain 'R' and resid 75 through 105 removed outlier: 3.956A pdb=" N PHE R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Proline residue: R 96 - end of helix Processing helix chain 'R' and resid 109 through 145 removed outlier: 4.351A pdb=" N LEU R 113 " --> pdb=" O TRP R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 153 Processing helix chain 'R' and resid 154 through 179 removed outlier: 4.576A pdb=" N LEU R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 186 through 195 Processing helix chain 'R' and resid 204 through 216 Processing helix chain 'R' and resid 216 through 242 Processing helix chain 'R' and resid 248 through 316 Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 321 through 335 removed outlier: 3.775A pdb=" N PHE R 325 " --> pdb=" O PRO R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 344 Processing helix chain 'R' and resid 346 through 357 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.612A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.725A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.128A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.561A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.314A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.577A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.733A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.854A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 200 removed outlier: 3.917A pdb=" N ALA A 229 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 230 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 276 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 232 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASN A 278 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 234 " --> pdb=" O ASN A 278 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1227 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: 3.89 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7723 1.03 - 1.23: 44 1.23 - 1.42: 3415 1.42 - 1.62: 4548 1.62 - 1.81: 70 Bond restraints: 15800 Sorted by residual: bond pdb=" N GLN N 1 " pdb=" H1 GLN N 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.437 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.416 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 1.457 1.491 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" CAE 5FW R 401 " pdb=" CAH 5FW R 401 " ideal model delta sigma weight residual 1.515 1.548 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 15795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 27651 1.29 - 2.57: 697 2.57 - 3.86: 39 3.86 - 5.14: 10 5.14 - 6.43: 3 Bond angle restraints: 28400 Sorted by residual: angle pdb=" CA LYS G 14 " pdb=" CB LYS G 14 " pdb=" CG LYS G 14 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 angle pdb=" C ARG G 13 " pdb=" N LYS G 14 " pdb=" CA LYS G 14 " ideal model delta sigma weight residual 121.94 117.16 4.78 2.00e+00 2.50e-01 5.72e+00 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 113.18 118.48 -5.30 2.37e+00 1.78e-01 5.00e+00 angle pdb=" CA GLN N 1 " pdb=" N GLN N 1 " pdb=" H1 GLN N 1 " ideal model delta sigma weight residual 120.00 113.57 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" CAJ 5FW R 401 " pdb=" CAG 5FW R 401 " pdb=" NAD 5FW R 401 " ideal model delta sigma weight residual 114.52 108.99 5.53 3.00e+00 1.11e-01 3.39e+00 ... (remaining 28395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6814 17.86 - 35.72: 446 35.72 - 53.58: 136 53.58 - 71.44: 35 71.44 - 89.30: 12 Dihedral angle restraints: 7443 sinusoidal: 3974 harmonic: 3469 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -116.96 30.96 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA LYS G 14 " pdb=" C LYS G 14 " pdb=" N LEU G 15 " pdb=" CA LEU G 15 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1067 0.055 - 0.111: 136 0.111 - 0.166: 31 0.166 - 0.221: 0 0.221 - 0.277: 1 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.57 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LYS G 14 " pdb=" N LYS G 14 " pdb=" C LYS G 14 " pdb=" CB LYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1232 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 56 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C VAL R 56 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 56 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA R 57 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 14 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LYS G 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LYS G 14 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU G 15 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 214 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C ARG A 214 " 0.021 2.00e-02 2.50e+03 pdb=" O ARG A 214 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP A 215 " -0.007 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 634 2.19 - 2.79: 31191 2.79 - 3.39: 42375 3.39 - 4.00: 56913 4.00 - 4.60: 87796 Nonbonded interactions: 218909 Sorted by model distance: nonbonded pdb=" HE1 TRP B 63 " pdb=" O GLY B 319 " model vdw 1.583 2.450 nonbonded pdb=" OE1 GLN N 53 " pdb=" H GLN N 53 " model vdw 1.672 2.450 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.678 2.450 nonbonded pdb=" OD1 ASP B 186 " pdb="HH11 ARG A 214 " model vdw 1.684 2.450 nonbonded pdb=" OD1 ASP B 66 " pdb=" H LEU B 69 " model vdw 1.687 2.450 ... (remaining 218904 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: 13.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.440 Find NCS groups from input model: 0.050 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:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.003 0.084 8054 Z= 0.145 Angle : 0.478 5.526 10919 Z= 0.277 Chirality : 0.040 0.277 1235 Planarity : 0.003 0.026 1389 Dihedral : 14.278 89.304 2885 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.78 % Allowed : 12.44 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 980 helix: -0.05 (0.24), residues: 388 sheet: -0.27 (0.36), residues: 195 loop : -1.61 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 8 TYR 0.008 0.001 TYR R 207 PHE 0.009 0.001 PHE R 225 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8051) covalent geometry : angle 0.47815 (10913) SS BOND : bond 0.00357 ( 3) SS BOND : angle 0.83152 ( 6) hydrogen bonds : bond 0.12321 ( 430) hydrogen bonds : angle 5.47215 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.6969 (ptm) cc_final: 0.6608 (mmm) REVERT: B 219 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7607 (mmt90) REVERT: N 43 LYS cc_start: 0.8416 (mttt) cc_final: 0.8122 (mttm) REVERT: N 50 ASP cc_start: 0.8072 (p0) cc_final: 0.7848 (p0) REVERT: A 25 LYS cc_start: 0.7479 (tttt) cc_final: 0.7257 (ttmm) REVERT: A 34 LYS cc_start: 0.7548 (tttt) cc_final: 0.7347 (tttm) REVERT: A 194 PHE cc_start: 0.7336 (m-80) cc_final: 0.6988 (m-80) REVERT: A 199 GLN cc_start: 0.8805 (tt0) cc_final: 0.8533 (tt0) REVERT: A 260 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7780 (ttpp) REVERT: A 266 ARG cc_start: 0.7853 (ptm160) cc_final: 0.7574 (ptm160) REVERT: A 330 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 333 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7712 (ttp80) REVERT: G 38 MET cc_start: 0.7797 (ttp) cc_final: 0.7573 (ttm) REVERT: G 42 GLU cc_start: 0.7328 (tt0) cc_final: 0.7119 (tp30) REVERT: R 73 GLN cc_start: 0.8402 (mt0) cc_final: 0.8094 (mt0) REVERT: R 290 LYS cc_start: 0.7378 (ttpt) cc_final: 0.7001 (mtmt) outliers start: 15 outliers final: 9 residues processed: 246 average time/residue: 1.2867 time to fit residues: 334.6584 Evaluate side-chains 209 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 155 ASN B 176 GLN B 340 ASN N 5 GLN G 24 ASN R 150 GLN R 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113275 restraints weight = 24821.170| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.85 r_work: 0.3112 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8054 Z= 0.204 Angle : 0.525 6.561 10919 Z= 0.294 Chirality : 0.042 0.136 1235 Planarity : 0.004 0.051 1389 Dihedral : 5.819 59.637 1111 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.79 % Allowed : 15.88 % Favored : 80.33 % 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 are not related in a simple way. whole: 0.01 (0.26), residues: 980 helix: 1.15 (0.26), residues: 379 sheet: 0.24 (0.35), residues: 206 loop : -1.23 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 317 TYR 0.010 0.001 TYR R 207 PHE 0.015 0.002 PHE A 232 TRP 0.011 0.002 TRP B 82 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8051) covalent geometry : angle 0.52445 (10913) SS BOND : bond 0.00632 ( 3) SS BOND : angle 1.29889 ( 6) hydrogen bonds : bond 0.05630 ( 430) hydrogen bonds : angle 4.74109 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.6449 (mpt90) REVERT: B 217 MET cc_start: 0.7801 (ptm) cc_final: 0.6634 (mmm) REVERT: B 219 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7913 (mmt90) REVERT: B 258 ASP cc_start: 0.8286 (t70) cc_final: 0.8022 (t70) REVERT: B 304 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8239 (ttp-110) REVERT: N 21 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8609 (m) REVERT: N 43 LYS cc_start: 0.8313 (mttt) cc_final: 0.7988 (mttm) REVERT: A 25 LYS cc_start: 0.7663 (tttt) cc_final: 0.7311 (ttmm) REVERT: A 199 GLN cc_start: 0.8919 (tt0) cc_final: 0.8679 (tt0) REVERT: A 260 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8186 (ttpt) REVERT: A 266 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7987 (ptm160) REVERT: A 330 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7642 (mm-30) REVERT: G 38 MET cc_start: 0.8001 (ttp) cc_final: 0.7760 (ttm) REVERT: G 42 GLU cc_start: 0.7862 (tt0) cc_final: 0.7396 (tp30) REVERT: R 73 GLN cc_start: 0.8569 (mt0) cc_final: 0.8320 (mt0) REVERT: R 77 ASN cc_start: 0.8956 (m-40) cc_final: 0.8748 (m110) REVERT: R 232 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8167 (ttp-170) REVERT: R 290 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7212 (mtmt) outliers start: 32 outliers final: 15 residues processed: 212 average time/residue: 1.3279 time to fit residues: 296.9023 Evaluate side-chains 205 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 151 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 155 ASN B 176 GLN B 340 ASN N 5 GLN R 59 ASN R 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115647 restraints weight = 24723.658| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.85 r_work: 0.3153 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8054 Z= 0.122 Angle : 0.463 6.091 10919 Z= 0.257 Chirality : 0.040 0.130 1235 Planarity : 0.004 0.047 1389 Dihedral : 5.599 59.822 1110 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.32 % Allowed : 17.77 % Favored : 78.91 % 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 are not related in a simple way. whole: 0.58 (0.26), residues: 980 helix: 1.70 (0.27), residues: 377 sheet: 0.59 (0.36), residues: 192 loop : -0.98 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 71 TYR 0.009 0.001 TYR R 207 PHE 0.012 0.001 PHE R 225 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8051) covalent geometry : angle 0.46280 (10913) SS BOND : bond 0.00357 ( 3) SS BOND : angle 0.83684 ( 6) hydrogen bonds : bond 0.04955 ( 430) hydrogen bonds : angle 4.48750 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.6344 (mpt90) REVERT: B 96 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: B 217 MET cc_start: 0.7783 (ptm) cc_final: 0.6616 (mmm) REVERT: B 219 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7693 (mmt90) REVERT: B 258 ASP cc_start: 0.8261 (t70) cc_final: 0.8058 (t70) REVERT: N 43 LYS cc_start: 0.8293 (mttt) cc_final: 0.7970 (mttm) REVERT: N 65 LYS cc_start: 0.7693 (tttm) cc_final: 0.7426 (mttm) REVERT: A 25 LYS cc_start: 0.7618 (tttt) cc_final: 0.7266 (ttmm) REVERT: A 27 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 199 GLN cc_start: 0.8932 (tt0) cc_final: 0.8685 (tt0) REVERT: A 260 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8135 (ttpt) REVERT: A 266 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7950 (ptm160) REVERT: A 330 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7688 (mm-30) REVERT: G 38 MET cc_start: 0.7913 (ttp) cc_final: 0.7704 (ttm) REVERT: G 42 GLU cc_start: 0.7820 (tt0) cc_final: 0.7356 (tp30) REVERT: R 73 GLN cc_start: 0.8538 (mt0) cc_final: 0.8310 (mt0) REVERT: R 77 ASN cc_start: 0.8881 (m-40) cc_final: 0.8646 (m110) REVERT: R 290 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7171 (mtmt) outliers start: 28 outliers final: 15 residues processed: 207 average time/residue: 1.3101 time to fit residues: 286.9140 Evaluate side-chains 200 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 77 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 5 GLN ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114471 restraints weight = 24597.697| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3131 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8054 Z= 0.160 Angle : 0.487 5.854 10919 Z= 0.271 Chirality : 0.041 0.130 1235 Planarity : 0.004 0.040 1389 Dihedral : 5.395 59.238 1105 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.20 % Allowed : 18.13 % Favored : 78.67 % 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 are not related in a simple way. whole: 0.73 (0.27), residues: 980 helix: 1.84 (0.27), residues: 378 sheet: 0.53 (0.35), residues: 204 loop : -0.87 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 71 TYR 0.010 0.001 TYR R 207 PHE 0.013 0.001 PHE R 225 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8051) covalent geometry : angle 0.48611 (10913) SS BOND : bond 0.00507 ( 3) SS BOND : angle 1.02879 ( 6) hydrogen bonds : bond 0.05222 ( 430) hydrogen bonds : angle 4.47282 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7924 (mtt180) REVERT: B 217 MET cc_start: 0.7793 (ptm) cc_final: 0.6646 (mmm) REVERT: B 219 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7758 (mmt90) REVERT: B 258 ASP cc_start: 0.8268 (t70) cc_final: 0.8033 (t70) REVERT: N 21 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (m) REVERT: N 43 LYS cc_start: 0.8282 (mttt) cc_final: 0.7957 (mttm) REVERT: A 25 LYS cc_start: 0.7632 (tttt) cc_final: 0.7268 (ttmm) REVERT: A 27 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 199 GLN cc_start: 0.8924 (tt0) cc_final: 0.8674 (tt0) REVERT: A 260 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8131 (ttpt) REVERT: A 266 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7964 (ptm160) REVERT: A 330 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7723 (mm-30) REVERT: G 38 MET cc_start: 0.7957 (ttp) cc_final: 0.7743 (ttm) REVERT: G 42 GLU cc_start: 0.7840 (tt0) cc_final: 0.7381 (tp30) REVERT: R 73 GLN cc_start: 0.8567 (mt0) cc_final: 0.8330 (mt0) REVERT: R 77 ASN cc_start: 0.8926 (m-40) cc_final: 0.8707 (m110) REVERT: R 185 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: R 290 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7192 (mtmt) outliers start: 27 outliers final: 16 residues processed: 203 average time/residue: 1.3010 time to fit residues: 279.4210 Evaluate side-chains 204 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 340 ASN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115129 restraints weight = 24550.509| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.84 r_work: 0.3130 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8054 Z= 0.147 Angle : 0.477 6.348 10919 Z= 0.266 Chirality : 0.040 0.129 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.437 59.024 1105 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.91 % Allowed : 17.30 % Favored : 78.79 % 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 are not related in a simple way. whole: 0.90 (0.27), residues: 980 helix: 2.01 (0.26), residues: 379 sheet: 0.50 (0.34), residues: 206 loop : -0.75 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.010 0.001 TYR R 207 PHE 0.013 0.001 PHE R 225 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8051) covalent geometry : angle 0.47610 (10913) SS BOND : bond 0.00495 ( 3) SS BOND : angle 1.02370 ( 6) hydrogen bonds : bond 0.05111 ( 430) hydrogen bonds : angle 4.41266 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7942 (mtt180) REVERT: B 214 ARG cc_start: 0.8236 (mpt90) cc_final: 0.7924 (mmt180) REVERT: B 217 MET cc_start: 0.7778 (ptm) cc_final: 0.6657 (mmm) REVERT: B 219 ARG cc_start: 0.8281 (mmt180) cc_final: 0.7777 (mmt90) REVERT: N 21 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8604 (m) REVERT: N 43 LYS cc_start: 0.8250 (mttt) cc_final: 0.7926 (mttm) REVERT: A 25 LYS cc_start: 0.7643 (tttt) cc_final: 0.7313 (ttmm) REVERT: A 27 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 195 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: A 199 GLN cc_start: 0.8919 (tt0) cc_final: 0.8672 (tt0) REVERT: A 266 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7975 (ptm160) REVERT: A 330 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7751 (mm-30) REVERT: G 14 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5348 (pttt) REVERT: G 38 MET cc_start: 0.7923 (ttp) cc_final: 0.7713 (ttm) REVERT: G 42 GLU cc_start: 0.7803 (tt0) cc_final: 0.7344 (tp30) REVERT: R 73 GLN cc_start: 0.8559 (mt0) cc_final: 0.8331 (mt0) REVERT: R 77 ASN cc_start: 0.8918 (m-40) cc_final: 0.8711 (m110) REVERT: R 290 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7187 (mtmt) outliers start: 33 outliers final: 14 residues processed: 205 average time/residue: 1.2382 time to fit residues: 269.0659 Evaluate side-chains 205 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115158 restraints weight = 24559.628| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.3133 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8054 Z= 0.144 Angle : 0.476 6.188 10919 Z= 0.265 Chirality : 0.040 0.129 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.400 58.827 1105 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.84 % Allowed : 19.43 % Favored : 77.73 % 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 are not related in a simple way. whole: 0.99 (0.27), residues: 980 helix: 2.14 (0.26), residues: 379 sheet: 0.52 (0.34), residues: 206 loop : -0.75 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 251 TYR 0.010 0.001 TYR R 207 PHE 0.013 0.001 PHE R 225 TRP 0.015 0.001 TRP B 339 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8051) covalent geometry : angle 0.47522 (10913) SS BOND : bond 0.00485 ( 3) SS BOND : angle 1.00526 ( 6) hydrogen bonds : bond 0.05067 ( 430) hydrogen bonds : angle 4.38136 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8018 (mt0) cc_final: 0.7540 (mm110) REVERT: B 96 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (mtt180) REVERT: B 217 MET cc_start: 0.7792 (ptm) cc_final: 0.6661 (mmm) REVERT: B 219 ARG cc_start: 0.8279 (mmt180) cc_final: 0.7792 (mmt90) REVERT: N 21 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8603 (m) REVERT: N 43 LYS cc_start: 0.8239 (mttt) cc_final: 0.7914 (mttm) REVERT: A 25 LYS cc_start: 0.7662 (tttt) cc_final: 0.7333 (ttmm) REVERT: A 27 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 199 GLN cc_start: 0.8920 (tt0) cc_final: 0.8672 (tt0) REVERT: A 266 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7990 (ptm160) REVERT: A 330 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7744 (mm-30) REVERT: G 14 LYS cc_start: 0.5819 (OUTLIER) cc_final: 0.5428 (pttt) REVERT: G 38 MET cc_start: 0.7933 (ttp) cc_final: 0.7723 (ttm) REVERT: G 42 GLU cc_start: 0.7802 (tt0) cc_final: 0.7355 (tp30) REVERT: R 73 GLN cc_start: 0.8557 (mt0) cc_final: 0.8331 (mt0) REVERT: R 77 ASN cc_start: 0.8916 (m-40) cc_final: 0.8711 (m110) REVERT: R 185 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: R 290 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7189 (mtmt) outliers start: 24 outliers final: 14 residues processed: 203 average time/residue: 1.1850 time to fit residues: 254.8888 Evaluate side-chains 206 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 340 ASN N 1 GLN N 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114426 restraints weight = 24459.653| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.85 r_work: 0.3130 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8054 Z= 0.149 Angle : 0.480 6.331 10919 Z= 0.268 Chirality : 0.041 0.129 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.423 58.250 1105 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.44 % Allowed : 19.55 % Favored : 77.01 % 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 are not related in a simple way. whole: 1.09 (0.27), residues: 980 helix: 2.24 (0.26), residues: 379 sheet: 0.61 (0.35), residues: 204 loop : -0.72 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.010 0.001 TYR R 207 PHE 0.013 0.001 PHE R 225 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8051) covalent geometry : angle 0.47921 (10913) SS BOND : bond 0.00503 ( 3) SS BOND : angle 1.02580 ( 6) hydrogen bonds : bond 0.05092 ( 430) hydrogen bonds : angle 4.36835 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8007 (mt0) cc_final: 0.7521 (mm110) REVERT: B 59 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: B 96 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7996 (mtt180) REVERT: B 214 ARG cc_start: 0.8240 (mpt90) cc_final: 0.7913 (mmt180) REVERT: B 217 MET cc_start: 0.7795 (ptm) cc_final: 0.6663 (mmm) REVERT: B 219 ARG cc_start: 0.8278 (mmt180) cc_final: 0.7801 (mmt90) REVERT: N 21 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8601 (m) REVERT: N 43 LYS cc_start: 0.8240 (mttt) cc_final: 0.7918 (mttm) REVERT: A 25 LYS cc_start: 0.7649 (tttt) cc_final: 0.7314 (ttmm) REVERT: A 27 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 199 GLN cc_start: 0.8911 (tt0) cc_final: 0.8661 (tt0) REVERT: A 330 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7674 (mm-30) REVERT: G 14 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5597 (pttt) REVERT: G 38 MET cc_start: 0.7936 (ttp) cc_final: 0.7729 (ttm) REVERT: G 42 GLU cc_start: 0.7809 (tt0) cc_final: 0.7364 (tp30) REVERT: R 73 GLN cc_start: 0.8552 (mt0) cc_final: 0.8328 (mt0) REVERT: R 185 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: R 290 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7179 (mtmt) outliers start: 29 outliers final: 14 residues processed: 203 average time/residue: 1.2401 time to fit residues: 266.6126 Evaluate side-chains 202 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN B 239 ASN B 293 ASN B 340 ASN N 5 GLN R 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114305 restraints weight = 24655.841| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.85 r_work: 0.3124 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8054 Z= 0.148 Angle : 0.478 6.316 10919 Z= 0.267 Chirality : 0.041 0.129 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.411 58.470 1105 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.84 % Allowed : 20.73 % Favored : 76.42 % 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 are not related in a simple way. whole: 1.04 (0.27), residues: 980 helix: 2.17 (0.26), residues: 385 sheet: 0.60 (0.35), residues: 205 loop : -0.78 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 71 TYR 0.010 0.001 TYR R 207 PHE 0.013 0.001 PHE R 225 TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8051) covalent geometry : angle 0.47741 (10913) SS BOND : bond 0.00503 ( 3) SS BOND : angle 1.02980 ( 6) hydrogen bonds : bond 0.05075 ( 430) hydrogen bonds : angle 4.35965 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8001 (mt0) cc_final: 0.7565 (mm110) REVERT: B 59 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8801 (m-80) REVERT: B 96 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7956 (mtt180) REVERT: B 214 ARG cc_start: 0.8210 (mpt90) cc_final: 0.7904 (mmt180) REVERT: B 217 MET cc_start: 0.7776 (ptm) cc_final: 0.6665 (mmm) REVERT: B 219 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7787 (mmt90) REVERT: N 21 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8597 (m) REVERT: N 43 LYS cc_start: 0.8228 (mttt) cc_final: 0.7904 (mttm) REVERT: A 25 LYS cc_start: 0.7652 (tttt) cc_final: 0.7315 (ttmm) REVERT: A 27 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 199 GLN cc_start: 0.8915 (tt0) cc_final: 0.8665 (tt0) REVERT: A 330 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7692 (mm-30) REVERT: G 14 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5705 (pttt) REVERT: G 38 MET cc_start: 0.7914 (ttp) cc_final: 0.7709 (ttm) REVERT: G 42 GLU cc_start: 0.7810 (tt0) cc_final: 0.7349 (tp30) REVERT: R 73 GLN cc_start: 0.8537 (mt0) cc_final: 0.8320 (mt0) REVERT: R 185 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: R 290 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7164 (mtmt) outliers start: 24 outliers final: 14 residues processed: 202 average time/residue: 1.3079 time to fit residues: 279.2785 Evaluate side-chains 204 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 ASN B 340 ASN N 5 GLN R 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113139 restraints weight = 24652.263| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.86 r_work: 0.3102 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8054 Z= 0.192 Angle : 0.510 6.790 10919 Z= 0.286 Chirality : 0.042 0.137 1235 Planarity : 0.004 0.040 1389 Dihedral : 5.541 59.858 1105 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.96 % Allowed : 20.62 % Favored : 76.42 % 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 are not related in a simple way. whole: 1.05 (0.27), residues: 980 helix: 2.19 (0.26), residues: 379 sheet: 0.59 (0.35), residues: 205 loop : -0.73 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 71 TYR 0.010 0.001 TYR R 207 PHE 0.015 0.002 PHE R 225 TRP 0.011 0.002 TRP A 220 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8051) covalent geometry : angle 0.50901 (10913) SS BOND : bond 0.00647 ( 3) SS BOND : angle 1.23458 ( 6) hydrogen bonds : bond 0.05542 ( 430) hydrogen bonds : angle 4.44711 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8002 (mt0) cc_final: 0.7563 (mm110) REVERT: B 59 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8811 (m-80) REVERT: B 214 ARG cc_start: 0.8218 (mpt90) cc_final: 0.7918 (mmt180) REVERT: B 217 MET cc_start: 0.7764 (ptm) cc_final: 0.6669 (mmm) REVERT: B 219 ARG cc_start: 0.8282 (mmt180) cc_final: 0.7812 (mmt90) REVERT: N 21 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8610 (m) REVERT: N 43 LYS cc_start: 0.8261 (mttt) cc_final: 0.7938 (mttm) REVERT: A 25 LYS cc_start: 0.7702 (tttt) cc_final: 0.7343 (ttmm) REVERT: A 27 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 199 GLN cc_start: 0.8922 (tt0) cc_final: 0.8670 (tt0) REVERT: A 330 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7742 (mm-30) REVERT: G 14 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5879 (pttt) REVERT: G 38 MET cc_start: 0.7970 (ttp) cc_final: 0.7756 (ttm) REVERT: G 42 GLU cc_start: 0.7836 (tt0) cc_final: 0.7380 (tp30) REVERT: R 73 GLN cc_start: 0.8564 (mt0) cc_final: 0.8332 (mt0) REVERT: R 185 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: R 290 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7170 (mtmt) outliers start: 25 outliers final: 15 residues processed: 199 average time/residue: 1.3221 time to fit residues: 277.6736 Evaluate side-chains 201 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN B 239 ASN B 340 ASN N 5 GLN R 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114557 restraints weight = 24750.778| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.85 r_work: 0.3125 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8054 Z= 0.149 Angle : 0.482 6.530 10919 Z= 0.269 Chirality : 0.041 0.131 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.429 58.375 1105 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.13 % Allowed : 21.68 % Favored : 76.18 % 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 are not related in a simple way. whole: 1.16 (0.27), residues: 980 helix: 2.30 (0.26), residues: 379 sheet: 0.58 (0.34), residues: 209 loop : -0.66 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.010 0.001 TYR R 207 PHE 0.014 0.001 PHE R 225 TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8051) covalent geometry : angle 0.48121 (10913) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.03127 ( 6) hydrogen bonds : bond 0.05132 ( 430) hydrogen bonds : angle 4.37459 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 44 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8001 (mt0) cc_final: 0.7571 (mm110) REVERT: B 59 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: B 214 ARG cc_start: 0.8215 (mpt90) cc_final: 0.7920 (mmt180) REVERT: B 217 MET cc_start: 0.7779 (ptm) cc_final: 0.6684 (mmm) REVERT: B 219 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7819 (mmt90) REVERT: N 21 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8601 (m) REVERT: N 43 LYS cc_start: 0.8255 (mttt) cc_final: 0.7932 (mttm) REVERT: A 25 LYS cc_start: 0.7662 (tttt) cc_final: 0.7310 (ttmm) REVERT: A 27 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 199 GLN cc_start: 0.8920 (tt0) cc_final: 0.8670 (tt0) REVERT: A 330 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7734 (mm-30) REVERT: G 38 MET cc_start: 0.7958 (ttp) cc_final: 0.7757 (ttm) REVERT: G 42 GLU cc_start: 0.7822 (tt0) cc_final: 0.7378 (tp30) REVERT: R 73 GLN cc_start: 0.8543 (mt0) cc_final: 0.8320 (mt0) REVERT: R 185 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: R 290 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7170 (mtmt) outliers start: 18 outliers final: 11 residues processed: 199 average time/residue: 1.3558 time to fit residues: 284.8258 Evaluate side-chains 200 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 185 GLU Chi-restraints excluded: chain R residue 308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN B 239 ASN B 340 ASN N 5 GLN R 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114980 restraints weight = 24907.127| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.77 r_work: 0.3129 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8054 Z= 0.143 Angle : 0.480 6.211 10919 Z= 0.267 Chirality : 0.041 0.130 1235 Planarity : 0.004 0.039 1389 Dihedral : 5.377 56.896 1105 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.25 % Allowed : 21.68 % Favored : 76.07 % 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 are not related in a simple way. whole: 1.14 (0.27), residues: 980 helix: 2.25 (0.26), residues: 385 sheet: 0.58 (0.34), residues: 209 loop : -0.67 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 71 TYR 0.012 0.001 TYR N 115 PHE 0.013 0.001 PHE R 225 TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8051) covalent geometry : angle 0.47984 (10913) SS BOND : bond 0.00502 ( 3) SS BOND : angle 1.01451 ( 6) hydrogen bonds : bond 0.05034 ( 430) hydrogen bonds : angle 4.34663 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7619.28 seconds wall clock time: 129 minutes 14.24 seconds (7754.24 seconds total)