Starting phenix.real_space_refine on Fri Jul 3 05:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkd_33248/07_2026/7xkd_33248.cif" } resolution = 2.4 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5427 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5087 2.51 5 N 1372 2.21 5 O 1455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2086 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'AND': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.80, per 1000 atoms: 0.23 Number of scatterers: 7962 At special positions: 0 Unit cell: (103.887, 109.242, 95.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1455 8.00 N 1372 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 410.1 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.550A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.547A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.576A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.520A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 25 removed outlier: 4.026A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 617 through 645 Processing helix chain 'R' and resid 646 through 649 Processing helix chain 'R' and resid 651 through 677 Processing helix chain 'R' and resid 682 through 716 Processing helix chain 'R' and resid 725 through 749 Proline residue: R 738 - end of helix Processing helix chain 'R' and resid 750 through 753 removed outlier: 3.781A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 776 through 783 Processing helix chain 'R' and resid 783 through 809 Processing helix chain 'R' and resid 820 through 834 removed outlier: 3.989A pdb=" N LEU R 824 " --> pdb=" O SER R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 835 through 838 Processing helix chain 'R' and resid 839 through 845 removed outlier: 4.145A pdb=" N PHE R 843 " --> pdb=" O GLY R 839 " (cutoff:3.500A) Processing helix chain 'R' and resid 849 through 862 removed outlier: 3.718A pdb=" N LEU R 862 " --> pdb=" O ILE R 858 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 883 removed outlier: 3.505A pdb=" N ARG R 879 " --> pdb=" O LYS R 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.476A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.631A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.791A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.718A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.745A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.587A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.853A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1283 1.31 - 1.44: 2278 1.44 - 1.56: 4493 1.56 - 1.69: 8 1.69 - 1.81: 66 Bond restraints: 8128 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.683 -0.351 2.00e-02 2.50e+03 3.09e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.741 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.682 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.660 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.642 -0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10705 1.68 - 3.37: 222 3.37 - 5.05: 61 5.05 - 6.74: 19 6.74 - 8.42: 6 Bond angle restraints: 11013 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.03 124.44 -4.41 9.90e-01 1.02e+00 1.99e+01 angle pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" CD PRO G 53 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 108.49 115.17 -6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 119.12 -5.59 1.39e+00 5.18e-01 1.62e+01 angle pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta sigma weight residual 119.05 123.35 -4.30 1.11e+00 8.12e-01 1.50e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4206 17.29 - 34.57: 455 34.57 - 51.86: 103 51.86 - 69.14: 22 69.14 - 86.43: 6 Dihedral angle restraints: 4792 sinusoidal: 1872 harmonic: 2920 Sorted by residual: 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 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -125.04 39.04 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1127 0.078 - 0.156: 112 0.156 - 0.235: 2 0.235 - 0.313: 1 0.313 - 0.391: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.74 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1240 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ARG N 98 " -0.084 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO G 53 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO N 14 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 37 2.45 - 3.06: 5344 3.06 - 3.67: 11902 3.67 - 4.29: 18288 4.29 - 4.90: 30575 Nonbonded interactions: 66146 Sorted by model distance: nonbonded pdb=" O CYS B 204 " pdb=" OD1 ASP B 228 " model vdw 1.832 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASN A 278 " pdb=" OG SER A 352 " model vdw 2.210 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.215 3.120 nonbonded pdb=" CA ASN A 279 " pdb=" OD2 ASP N 106 " model vdw 2.217 3.470 ... (remaining 66141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:7.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.007 0.351 8131 Z= 0.332 Angle : 0.682 8.425 11019 Z= 0.378 Chirality : 0.046 0.391 1243 Planarity : 0.006 0.112 1394 Dihedral : 15.160 85.281 2897 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.94 % Allowed : 17.22 % Favored : 81.84 % 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: 0.77 (0.27), residues: 988 helix: 2.40 (0.26), residues: 375 sheet: -0.04 (0.33), residues: 229 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 13 TYR 0.012 0.001 TYR N 60 PHE 0.012 0.001 PHE R 634 TRP 0.014 0.001 TRP A 234 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.33 ( 8128) covalent geometry : angle 0.68226 / 0.38 (11013) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 0.94739 / 0.53 ( 6) hydrogen bonds : bond 0.13355 / 9.14 ( 401) hydrogen bonds : angle 5.37840 / 3.80 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8813 (mm110) cc_final: 0.8095 (pt0) REVERT: A 381 ASP cc_start: 0.8517 (t70) cc_final: 0.8103 (t70) REVERT: G 13 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7964 (mtm110) outliers start: 8 outliers final: 7 residues processed: 166 average time/residue: 0.7103 time to fit residues: 123.6811 Evaluate side-chains 133 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066940 restraints weight = 14537.645| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.93 r_work: 0.2772 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8131 Z= 0.163 Angle : 0.574 6.233 11019 Z= 0.311 Chirality : 0.043 0.155 1243 Planarity : 0.004 0.066 1394 Dihedral : 5.135 46.827 1115 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.54 % Allowed : 19.81 % Favored : 76.65 % 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: 0.88 (0.27), residues: 988 helix: 2.53 (0.26), residues: 373 sheet: 0.06 (0.34), residues: 220 loop : -1.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 650 TYR 0.017 0.001 TYR A 339 PHE 0.013 0.001 PHE R 634 TRP 0.015 0.001 TRP B 211 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 8128) covalent geometry : angle 0.56878 / 0.31 (11013) SS BOND : bond 0.00591 / 0.28 ( 3) SS BOND : angle 3.42907 / 1.85 ( 6) hydrogen bonds : bond 0.04502 / 3.11 ( 401) hydrogen bonds : angle 4.36730 / 3.10 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.338 Fit side-chains REVERT: A 12 GLN cc_start: 0.8265 (mm110) cc_final: 0.7838 (pt0) REVERT: A 38 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8390 (mmt90) REVERT: A 216 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8861 (mmpt) REVERT: A 220 HIS cc_start: 0.8689 (m170) cc_final: 0.8415 (m170) REVERT: A 296 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 381 ASP cc_start: 0.9004 (t70) cc_final: 0.8606 (t70) REVERT: B 23 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8628 (tppt) REVERT: B 61 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9080 (ppp) REVERT: G 13 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8164 (mtm110) REVERT: G 47 GLU cc_start: 0.8742 (pm20) cc_final: 0.8473 (pm20) REVERT: G 58 GLU cc_start: 0.8324 (pm20) cc_final: 0.8094 (pm20) REVERT: R 646 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7395 (tm-30) outliers start: 30 outliers final: 9 residues processed: 154 average time/residue: 0.6456 time to fit residues: 104.9307 Evaluate side-chains 142 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.067756 restraints weight = 14333.516| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.90 r_work: 0.2785 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8131 Z= 0.139 Angle : 0.547 7.715 11019 Z= 0.292 Chirality : 0.042 0.152 1243 Planarity : 0.004 0.055 1394 Dihedral : 4.415 36.620 1105 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.66 % Allowed : 20.28 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.27), residues: 988 helix: 2.54 (0.26), residues: 374 sheet: 0.01 (0.34), residues: 221 loop : -1.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.012 0.001 TYR A 339 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8128) covalent geometry : angle 0.54304 / 0.29 (11013) SS BOND : bond 0.00406 / 0.20 ( 3) SS BOND : angle 2.69051 / 1.43 ( 6) hydrogen bonds : bond 0.04206 / 2.91 ( 401) hydrogen bonds : angle 4.23132 / 3.00 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.331 Fit side-chains REVERT: A 12 GLN cc_start: 0.8324 (mm110) cc_final: 0.7804 (pt0) REVERT: A 13 ARG cc_start: 0.8187 (mpt180) cc_final: 0.7954 (mtm-85) REVERT: A 38 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8346 (mmt90) REVERT: A 216 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8909 (mmpt) REVERT: B 10 GLU cc_start: 0.8555 (tp30) cc_final: 0.8291 (tp30) REVERT: B 23 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8617 (tppt) REVERT: B 61 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9144 (ppp) REVERT: B 215 GLU cc_start: 0.8885 (pm20) cc_final: 0.8684 (pm20) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7555 (t80) REVERT: G 47 GLU cc_start: 0.8729 (pm20) cc_final: 0.8496 (pm20) REVERT: N 3 GLN cc_start: 0.8394 (tt0) cc_final: 0.8164 (tt0) REVERT: R 646 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7289 (tm-30) outliers start: 31 outliers final: 12 residues processed: 162 average time/residue: 0.6468 time to fit residues: 110.5220 Evaluate side-chains 139 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 668 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.068621 restraints weight = 14677.574| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.96 r_work: 0.2805 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8131 Z= 0.122 Angle : 0.548 6.240 11019 Z= 0.292 Chirality : 0.041 0.142 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.330 34.605 1105 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.77 % Allowed : 20.75 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.88 (0.27), residues: 988 helix: 2.52 (0.26), residues: 374 sheet: 0.03 (0.34), residues: 221 loop : -1.02 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.011 0.001 TYR A 339 PHE 0.010 0.001 PHE R 865 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8128) covalent geometry : angle 0.54544 / 0.29 (11013) SS BOND : bond 0.00438 / 0.21 ( 3) SS BOND : angle 2.47629 / 1.32 ( 6) hydrogen bonds : bond 0.03955 / 2.73 ( 401) hydrogen bonds : angle 4.16297 / 2.95 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.317 Fit side-chains REVERT: A 12 GLN cc_start: 0.8284 (mm110) cc_final: 0.7833 (pt0) REVERT: A 38 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8327 (mmt90) REVERT: A 216 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8935 (mmpt) REVERT: B 10 GLU cc_start: 0.8601 (tp30) cc_final: 0.8207 (tp30) REVERT: B 23 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8627 (tppt) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7545 (t80) REVERT: B 256 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7440 (ptt-90) REVERT: G 13 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8232 (mtm110) REVERT: G 47 GLU cc_start: 0.8683 (pm20) cc_final: 0.8390 (pm20) REVERT: R 646 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7248 (tm-30) REVERT: R 650 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8246 (mmt90) outliers start: 32 outliers final: 15 residues processed: 150 average time/residue: 0.6411 time to fit residues: 101.2289 Evaluate side-chains 145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069188 restraints weight = 14639.538| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.95 r_work: 0.2817 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8131 Z= 0.118 Angle : 0.550 6.289 11019 Z= 0.292 Chirality : 0.041 0.149 1243 Planarity : 0.004 0.050 1394 Dihedral : 4.251 33.684 1105 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.01 % Allowed : 22.05 % Favored : 73.94 % 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: 0.91 (0.27), residues: 988 helix: 2.53 (0.26), residues: 375 sheet: 0.08 (0.34), residues: 221 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 105 TYR 0.010 0.001 TYR N 60 PHE 0.010 0.001 PHE A 212 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8128) covalent geometry : angle 0.54742 / 0.29 (11013) SS BOND : bond 0.00367 / 0.18 ( 3) SS BOND : angle 2.17898 / 1.15 ( 6) hydrogen bonds : bond 0.03850 / 2.66 ( 401) hydrogen bonds : angle 4.09869 / 2.90 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8249 (mm110) cc_final: 0.7829 (pt0) REVERT: A 13 ARG cc_start: 0.8069 (mpt180) cc_final: 0.7536 (mpp-170) REVERT: A 38 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8343 (mmt90) REVERT: A 216 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8973 (mmpt) REVERT: B 10 GLU cc_start: 0.8591 (tp30) cc_final: 0.8169 (tp30) REVERT: B 23 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8644 (tppt) REVERT: B 127 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8671 (ptpt) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.7632 (t80) REVERT: B 256 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7625 (ptt-90) REVERT: G 47 GLU cc_start: 0.8702 (pm20) cc_final: 0.8446 (pm20) REVERT: R 646 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7192 (tm-30) REVERT: R 862 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7938 (pp) outliers start: 34 outliers final: 15 residues processed: 164 average time/residue: 0.5835 time to fit residues: 101.0525 Evaluate side-chains 143 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.068990 restraints weight = 14490.414| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.94 r_work: 0.2815 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8131 Z= 0.125 Angle : 0.565 7.672 11019 Z= 0.299 Chirality : 0.042 0.139 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.225 33.334 1105 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.25 % Allowed : 22.64 % Favored : 73.11 % 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: 0.88 (0.27), residues: 988 helix: 2.48 (0.26), residues: 375 sheet: 0.12 (0.34), residues: 221 loop : -1.04 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 650 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.013 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8128) covalent geometry : angle 0.56309 / 0.30 (11013) SS BOND : bond 0.00323 / 0.16 ( 3) SS BOND : angle 2.18666 / 1.16 ( 6) hydrogen bonds : bond 0.03864 / 2.67 ( 401) hydrogen bonds : angle 4.13424 / 2.94 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.223 Fit side-chains REVERT: A 12 GLN cc_start: 0.8230 (mm110) cc_final: 0.7821 (pt0) REVERT: A 13 ARG cc_start: 0.8086 (mpt180) cc_final: 0.7463 (mpp-170) REVERT: A 38 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8331 (mmt90) REVERT: A 216 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8970 (mmpt) REVERT: B 10 GLU cc_start: 0.8626 (tp30) cc_final: 0.8157 (tp30) REVERT: B 23 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8667 (tppt) REVERT: B 127 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8734 (ptpt) REVERT: B 234 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.7522 (t80) REVERT: G 13 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8081 (mtm110) REVERT: G 47 GLU cc_start: 0.8702 (pm20) cc_final: 0.8455 (pm20) REVERT: R 646 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7192 (tm-30) REVERT: R 862 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7969 (pp) outliers start: 36 outliers final: 20 residues processed: 153 average time/residue: 0.6209 time to fit residues: 100.0790 Evaluate side-chains 152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 31 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.069139 restraints weight = 14544.907| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.91 r_work: 0.2815 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8131 Z= 0.130 Angle : 0.578 7.323 11019 Z= 0.307 Chirality : 0.042 0.138 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.268 33.160 1105 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.89 % Allowed : 23.11 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.88 (0.27), residues: 988 helix: 2.45 (0.26), residues: 376 sheet: 0.09 (0.34), residues: 221 loop : -1.00 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 105 TYR 0.009 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.021 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8128) covalent geometry : angle 0.57561 / 0.31 (11013) SS BOND : bond 0.00487 / 0.23 ( 3) SS BOND : angle 2.53159 / 1.35 ( 6) hydrogen bonds : bond 0.03852 / 2.66 ( 401) hydrogen bonds : angle 4.11000 / 2.91 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.323 Fit side-chains REVERT: A 12 GLN cc_start: 0.8233 (mm110) cc_final: 0.7788 (pt0) REVERT: A 13 ARG cc_start: 0.8099 (mpt180) cc_final: 0.7572 (mtm-85) REVERT: A 38 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8334 (mmt90) REVERT: A 216 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8977 (mmpt) REVERT: B 10 GLU cc_start: 0.8644 (tp30) cc_final: 0.8168 (tp30) REVERT: B 23 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8696 (tppt) REVERT: B 127 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8721 (ptpt) REVERT: B 215 GLU cc_start: 0.8864 (pm20) cc_final: 0.8610 (pm20) REVERT: B 234 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.7535 (t80) REVERT: G 13 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8122 (mtm110) REVERT: G 20 LYS cc_start: 0.8260 (pttm) cc_final: 0.8051 (pttm) REVERT: G 47 GLU cc_start: 0.8710 (pm20) cc_final: 0.8459 (pm20) REVERT: R 768 ASP cc_start: 0.5605 (p0) cc_final: 0.5006 (m-30) REVERT: R 822 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8062 (tm-30) REVERT: R 862 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7944 (pp) outliers start: 33 outliers final: 19 residues processed: 152 average time/residue: 0.6153 time to fit residues: 98.8832 Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 744 ILE Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069170 restraints weight = 14533.887| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.92 r_work: 0.2818 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8131 Z= 0.129 Angle : 0.578 7.119 11019 Z= 0.307 Chirality : 0.042 0.141 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.248 33.522 1105 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.30 % Allowed : 23.58 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.89 (0.27), residues: 988 helix: 2.48 (0.26), residues: 376 sheet: 0.10 (0.34), residues: 220 loop : -1.01 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.021 0.001 TRP R 676 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8128) covalent geometry : angle 0.57557 / 0.31 (11013) SS BOND : bond 0.00433 / 0.21 ( 3) SS BOND : angle 2.47837 / 1.31 ( 6) hydrogen bonds : bond 0.03825 / 2.65 ( 401) hydrogen bonds : angle 4.09261 / 2.89 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.314 Fit side-chains REVERT: A 12 GLN cc_start: 0.8219 (mm110) cc_final: 0.7834 (pt0) REVERT: A 13 ARG cc_start: 0.8105 (mpt180) cc_final: 0.7575 (mtm-85) REVERT: A 38 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8326 (mmt90) REVERT: A 216 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8974 (mmpt) REVERT: B 10 GLU cc_start: 0.8628 (tp30) cc_final: 0.8133 (tp30) REVERT: B 23 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8693 (tppt) REVERT: B 127 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (ptpt) REVERT: B 234 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.7531 (t80) REVERT: G 20 LYS cc_start: 0.8222 (pttm) cc_final: 0.7984 (pttm) REVERT: G 47 GLU cc_start: 0.8722 (pm20) cc_final: 0.8468 (pm20) REVERT: R 822 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8058 (tm-30) REVERT: R 862 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7927 (pp) outliers start: 28 outliers final: 19 residues processed: 146 average time/residue: 0.6126 time to fit residues: 94.1636 Evaluate side-chains 152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068368 restraints weight = 14490.578| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.93 r_work: 0.2796 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8131 Z= 0.151 Angle : 0.611 8.596 11019 Z= 0.324 Chirality : 0.042 0.156 1243 Planarity : 0.004 0.057 1394 Dihedral : 4.327 34.193 1105 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.18 % Allowed : 24.06 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.81 (0.27), residues: 988 helix: 2.36 (0.26), residues: 376 sheet: 0.05 (0.34), residues: 221 loop : -1.00 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 13 TYR 0.009 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.022 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8128) covalent geometry : angle 0.60850 / 0.32 (11013) SS BOND : bond 0.00477 / 0.23 ( 3) SS BOND : angle 2.62210 / 1.38 ( 6) hydrogen bonds : bond 0.03979 / 2.75 ( 401) hydrogen bonds : angle 4.14304 / 2.92 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.316 Fit side-chains REVERT: A 12 GLN cc_start: 0.8203 (mm110) cc_final: 0.7900 (pt0) REVERT: A 13 ARG cc_start: 0.8184 (mpt180) cc_final: 0.7645 (mtm-85) REVERT: A 38 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8337 (mmt90) REVERT: A 216 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8983 (mmpt) REVERT: B 10 GLU cc_start: 0.8631 (tp30) cc_final: 0.8134 (tp30) REVERT: B 127 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8711 (ptpt) REVERT: B 215 GLU cc_start: 0.8780 (pm20) cc_final: 0.8179 (pm20) REVERT: B 217 MET cc_start: 0.7442 (pmt) cc_final: 0.6737 (pmt) REVERT: B 234 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.7467 (t80) REVERT: G 20 LYS cc_start: 0.8207 (pttm) cc_final: 0.7942 (pttm) REVERT: G 47 GLU cc_start: 0.8745 (pm20) cc_final: 0.8454 (pm20) REVERT: R 803 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: R 822 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8062 (tm-30) REVERT: R 862 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (pp) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 0.5650 time to fit residues: 88.4166 Evaluate side-chains 145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.092711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069013 restraints weight = 14456.975| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.85 r_work: 0.2864 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8131 Z= 0.173 Angle : 0.641 8.493 11019 Z= 0.339 Chirality : 0.043 0.167 1243 Planarity : 0.004 0.058 1394 Dihedral : 4.466 35.518 1105 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.07 % Allowed : 24.06 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.74 (0.27), residues: 988 helix: 2.30 (0.26), residues: 376 sheet: -0.03 (0.34), residues: 223 loop : -1.01 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 13 TYR 0.010 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.022 0.001 TRP R 676 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 8128) covalent geometry : angle 0.63751 / 0.34 (11013) SS BOND : bond 0.00530 / 0.26 ( 3) SS BOND : angle 2.87418 / 1.52 ( 6) hydrogen bonds : bond 0.04214 / 2.91 ( 401) hydrogen bonds : angle 4.24683 / 2.99 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.312 Fit side-chains REVERT: A 12 GLN cc_start: 0.8242 (mm110) cc_final: 0.7901 (pt0) REVERT: A 13 ARG cc_start: 0.8223 (mpt180) cc_final: 0.7661 (mtm-85) REVERT: A 38 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8395 (mmt90) REVERT: B 10 GLU cc_start: 0.8661 (tp30) cc_final: 0.8197 (tp30) REVERT: B 127 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8703 (ptpt) REVERT: B 234 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.7536 (t80) REVERT: G 13 ARG cc_start: 0.8467 (mtm110) cc_final: 0.8103 (mtm110) REVERT: G 20 LYS cc_start: 0.8286 (pttm) cc_final: 0.8020 (pttm) REVERT: G 47 GLU cc_start: 0.8762 (pm20) cc_final: 0.8480 (pm20) REVERT: R 803 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: R 822 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8080 (tm-30) REVERT: R 862 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (pp) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 0.5937 time to fit residues: 92.1024 Evaluate side-chains 148 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 810 LYS Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 862 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070431 restraints weight = 14382.253| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.86 r_work: 0.2899 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8131 Z= 0.139 Angle : 0.632 7.764 11019 Z= 0.334 Chirality : 0.043 0.171 1243 Planarity : 0.004 0.059 1394 Dihedral : 4.371 33.747 1105 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.48 % Allowed : 24.76 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.74 (0.27), residues: 988 helix: 2.26 (0.26), residues: 376 sheet: 0.01 (0.34), residues: 221 loop : -0.98 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.009 0.001 TYR A 339 PHE 0.011 0.001 PHE A 212 TRP 0.024 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8128) covalent geometry : angle 0.62998 / 0.33 (11013) SS BOND : bond 0.00442 / 0.21 ( 3) SS BOND : angle 2.42959 / 1.28 ( 6) hydrogen bonds : bond 0.03981 / 2.77 ( 401) hydrogen bonds : angle 4.23696 / 3.02 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.05 seconds wall clock time: 58 minutes 32.96 seconds (3512.96 seconds total)