Starting phenix.real_space_refine on Wed Feb 4 18:37:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkd_33248/02_2026/7xkd_33248.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkd_33248/02_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_33248/02_2026/7xkd_33248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkd_33248/02_2026/7xkd_33248.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkd_33248/02_2026/7xkd_33248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkd_33248/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.99, per 1000 atoms: 0.25 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: 0.50 Conformation dependent library (CDL) restraints added in 201.9 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: 0.28 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: 0.92 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: 4245 17.29 - 34.57: 464 34.57 - 51.86: 103 51.86 - 69.14: 22 69.14 - 86.43: 6 Dihedral angle restraints: 4840 sinusoidal: 1920 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 4837 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.020 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 15.111 85.281 2945 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 covalent geometry : bond 0.00687 ( 8128) covalent geometry : angle 0.68226 (11013) SS BOND : bond 0.00162 ( 3) SS BOND : angle 0.94739 ( 6) hydrogen bonds : bond 0.13355 ( 401) hydrogen bonds : angle 5.37840 ( 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 : 0.312 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: 0.6720 time to fit residues: 116.9818 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.091070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066949 restraints weight = 14544.849| |-----------------------------------------------------------------------------| r_work (start): 0.2914 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: 0.8328 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8131 Z= 0.164 Angle : 0.578 7.381 11019 Z= 0.312 Chirality : 0.043 0.151 1243 Planarity : 0.004 0.067 1394 Dihedral : 5.046 46.041 1163 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.19 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: 0.87 (0.27), residues: 988 helix: 2.52 (0.26), residues: 373 sheet: 0.00 (0.33), residues: 222 loop : -1.03 (0.30), residues: 393 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 covalent geometry : bond 0.00373 ( 8128) covalent geometry : angle 0.57026 (11013) SS BOND : bond 0.01108 ( 3) SS BOND : angle 4.00717 ( 6) hydrogen bonds : bond 0.04587 ( 401) hydrogen bonds : angle 4.39102 ( 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 : 0.342 Fit side-chains REVERT: A 12 GLN cc_start: 0.8253 (mm110) cc_final: 0.7839 (pt0) REVERT: A 38 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8389 (mmt90) REVERT: A 216 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8865 (mmpt) REVERT: A 220 HIS cc_start: 0.8690 (m170) cc_final: 0.8418 (m170) REVERT: A 296 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 381 ASP cc_start: 0.9000 (t70) cc_final: 0.8602 (t70) REVERT: B 23 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8626 (tppt) REVERT: B 61 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9076 (ppp) REVERT: G 13 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8177 (mtm110) REVERT: G 47 GLU cc_start: 0.8744 (pm20) cc_final: 0.8431 (pm20) REVERT: G 58 GLU cc_start: 0.8311 (pm20) cc_final: 0.8095 (pm20) REVERT: R 646 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 30 outliers final: 9 residues processed: 154 average time/residue: 0.6346 time to fit residues: 102.9262 Evaluate side-chains 140 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3393 r_free = 0.3393 target = 0.092517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068329 restraints weight = 14280.214| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.94 r_work: 0.2803 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8131 Z= 0.123 Angle : 0.535 7.700 11019 Z= 0.287 Chirality : 0.042 0.145 1243 Planarity : 0.004 0.055 1394 Dihedral : 4.268 35.923 1153 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.89 % Allowed : 20.40 % Favored : 75.71 % 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: 2.58 (0.26), residues: 373 sheet: 0.01 (0.34), residues: 221 loop : -1.02 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 650 TYR 0.011 0.001 TYR A 339 PHE 0.010 0.001 PHE A 212 TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8128) covalent geometry : angle 0.53246 (11013) SS BOND : bond 0.00362 ( 3) SS BOND : angle 2.41825 ( 6) hydrogen bonds : bond 0.04064 ( 401) hydrogen bonds : angle 4.20612 ( 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 172 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.325 Fit side-chains REVERT: A 12 GLN cc_start: 0.8332 (mm110) cc_final: 0.7918 (pt0) REVERT: A 13 ARG cc_start: 0.8193 (mpt180) cc_final: 0.7993 (mpp-170) REVERT: A 38 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8324 (mmt90) REVERT: A 216 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8912 (mmpt) REVERT: B 10 GLU cc_start: 0.8532 (tp30) cc_final: 0.8280 (tp30) REVERT: B 23 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8608 (tppt) REVERT: B 234 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.7569 (t80) REVERT: G 13 ARG cc_start: 0.8437 (mtm110) cc_final: 0.8227 (mtm110) REVERT: G 47 GLU cc_start: 0.8722 (pm20) cc_final: 0.8412 (pm20) REVERT: N 3 GLN cc_start: 0.8388 (tt0) cc_final: 0.8163 (tt0) REVERT: R 646 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7274 (tm-30) outliers start: 33 outliers final: 11 residues processed: 164 average time/residue: 0.6666 time to fit residues: 114.9436 Evaluate side-chains 137 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3332 r_free = 0.3332 target = 0.089007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.064492 restraints weight = 14777.463| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.96 r_work: 0.2716 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8131 Z= 0.230 Angle : 0.611 6.569 11019 Z= 0.325 Chirality : 0.044 0.156 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.599 38.411 1153 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.13 % Allowed : 20.75 % Favored : 75.12 % 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: 2.43 (0.26), residues: 376 sheet: -0.04 (0.33), residues: 223 loop : -1.03 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.018 0.001 TYR A 339 PHE 0.013 0.002 PHE R 634 TRP 0.015 0.001 TRP A 234 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 8128) covalent geometry : angle 0.60548 (11013) SS BOND : bond 0.00592 ( 3) SS BOND : angle 3.54359 ( 6) hydrogen bonds : bond 0.04706 ( 401) hydrogen bonds : angle 4.33366 ( 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 162 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8357 (mm110) cc_final: 0.7848 (pt0) REVERT: A 38 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8460 (mmt90) REVERT: A 216 LYS cc_start: 0.9160 (mtmm) cc_final: 0.8871 (mmpt) REVERT: B 10 GLU cc_start: 0.8643 (tp30) cc_final: 0.8234 (tp30) REVERT: B 23 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8668 (tppt) REVERT: B 127 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8769 (ptpt) REVERT: B 234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.7520 (t80) REVERT: B 256 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7682 (ptt-90) REVERT: G 47 GLU cc_start: 0.8766 (pm20) cc_final: 0.8499 (pm20) REVERT: G 58 GLU cc_start: 0.8298 (pm20) cc_final: 0.8087 (pm20) REVERT: R 646 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7250 (tm-30) REVERT: R 732 ILE cc_start: 0.8326 (mm) cc_final: 0.8106 (mt) REVERT: R 822 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8059 (tm-30) REVERT: R 862 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8044 (pp) outliers start: 35 outliers final: 14 residues processed: 152 average time/residue: 0.6803 time to fit residues: 108.6879 Evaluate side-chains 145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 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 862 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: 2.9990 chunk 25 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 849 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 = 0.3406 r_free = 0.3406 target = 0.092424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.068486 restraints weight = 14628.759| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.88 r_work: 0.2856 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1742 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= 0.151 Angle : 0.557 5.908 11019 Z= 0.298 Chirality : 0.042 0.147 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.433 35.964 1153 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.42 % Allowed : 22.52 % Favored : 74.06 % 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: 0.82 (0.27), residues: 988 helix: 2.45 (0.26), residues: 374 sheet: -0.04 (0.33), residues: 223 loop : -1.01 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.014 0.001 TYR A 339 PHE 0.011 0.001 PHE R 634 TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8128) covalent geometry : angle 0.55417 (11013) SS BOND : bond 0.00356 ( 3) SS BOND : angle 2.62402 ( 6) hydrogen bonds : bond 0.04251 ( 401) hydrogen bonds : angle 4.23486 ( 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 163 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8377 (mm110) cc_final: 0.7899 (pt0) REVERT: A 13 ARG cc_start: 0.8141 (mpt180) cc_final: 0.7617 (mpp-170) REVERT: A 38 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8431 (mmt90) REVERT: A 216 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8928 (mmpt) REVERT: B 10 GLU cc_start: 0.8678 (tp30) cc_final: 0.8234 (tp30) REVERT: B 23 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8720 (tppt) REVERT: B 234 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.7537 (t80) REVERT: B 256 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7556 (ptt-90) REVERT: G 47 GLU cc_start: 0.8776 (pm20) cc_final: 0.8529 (pm20) REVERT: R 646 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7182 (tm-30) REVERT: R 732 ILE cc_start: 0.8379 (mm) cc_final: 0.8157 (mt) REVERT: R 822 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8064 (tm-30) outliers start: 29 outliers final: 16 residues processed: 158 average time/residue: 0.5526 time to fit residues: 91.9522 Evaluate side-chains 141 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 198 LEU 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 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 810 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.070489 restraints weight = 14415.250| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.86 r_work: 0.2898 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1872 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= 0.121 Angle : 0.553 6.429 11019 Z= 0.297 Chirality : 0.042 0.151 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.240 34.034 1153 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.13 % Allowed : 21.82 % Favored : 74.06 % 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: 0.86 (0.27), residues: 988 helix: 2.48 (0.26), residues: 374 sheet: 0.06 (0.34), residues: 220 loop : -1.03 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.009 0.001 TYR A 339 PHE 0.013 0.001 PHE R 769 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8128) covalent geometry : angle 0.55070 (11013) SS BOND : bond 0.00321 ( 3) SS BOND : angle 2.18683 ( 6) hydrogen bonds : bond 0.03886 ( 401) hydrogen bonds : angle 4.15179 ( 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 175 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8398 (mm110) cc_final: 0.7820 (pt0) REVERT: A 13 ARG cc_start: 0.8133 (mpt180) cc_final: 0.7499 (mpp-170) REVERT: A 38 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8375 (mmt90) REVERT: A 216 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8961 (mmpt) REVERT: B 10 GLU cc_start: 0.8657 (tp30) cc_final: 0.8156 (tp30) REVERT: B 127 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8683 (ptpt) REVERT: B 215 GLU cc_start: 0.8881 (pm20) cc_final: 0.8670 (pm20) REVERT: B 234 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.7602 (t80) REVERT: G 20 LYS cc_start: 0.8383 (pttm) cc_final: 0.8108 (pttm) REVERT: G 47 GLU cc_start: 0.8737 (pm20) cc_final: 0.8463 (pm20) REVERT: R 623 ILE cc_start: 0.9159 (mm) cc_final: 0.8954 (mp) REVERT: R 646 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7265 (tm-30) REVERT: R 862 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8044 (pp) outliers start: 35 outliers final: 18 residues processed: 168 average time/residue: 0.5463 time to fit residues: 96.8736 Evaluate side-chains 156 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 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 848 VAL 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3445 r_free = 0.3445 target = 0.094938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.071156 restraints weight = 14465.101| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.86 r_work: 0.2915 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8131 Z= 0.119 Angle : 0.566 7.726 11019 Z= 0.298 Chirality : 0.041 0.140 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.187 33.245 1153 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.77 % Allowed : 23.11 % 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: 2.50 (0.26), residues: 375 sheet: 0.09 (0.34), residues: 220 loop : -1.04 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 105 TYR 0.010 0.001 TYR N 60 PHE 0.011 0.001 PHE A 212 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8128) covalent geometry : angle 0.56291 (11013) SS BOND : bond 0.00395 ( 3) SS BOND : angle 2.40370 ( 6) hydrogen bonds : bond 0.03764 ( 401) hydrogen bonds : angle 4.09133 ( 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 170 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8308 (mm110) cc_final: 0.7827 (pt0) REVERT: A 13 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7555 (mpp-170) REVERT: A 38 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8367 (mmt90) REVERT: A 216 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8946 (mmpt) REVERT: B 10 GLU cc_start: 0.8656 (tp30) cc_final: 0.8151 (tp30) REVERT: B 127 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8688 (ptpt) REVERT: B 234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.7670 (t80) REVERT: G 20 LYS cc_start: 0.8380 (pttm) cc_final: 0.8163 (pttm) REVERT: G 47 GLU cc_start: 0.8726 (pm20) cc_final: 0.8450 (pm20) REVERT: R 646 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7054 (tm-30) REVERT: R 822 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8080 (tm-30) REVERT: R 862 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8026 (pp) outliers start: 32 outliers final: 17 residues processed: 160 average time/residue: 0.6082 time to fit residues: 102.4109 Evaluate side-chains 147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 331 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3438 r_free = 0.3438 target = 0.094350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070637 restraints weight = 14494.638| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.85 r_work: 0.2915 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1965 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= 0.135 Angle : 0.592 7.206 11019 Z= 0.313 Chirality : 0.042 0.141 1243 Planarity : 0.004 0.053 1394 Dihedral : 4.207 33.653 1153 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.18 % Allowed : 23.94 % 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: 0.91 (0.27), residues: 988 helix: 2.50 (0.26), residues: 375 sheet: 0.08 (0.34), residues: 221 loop : -0.98 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 105 TYR 0.012 0.001 TYR N 60 PHE 0.010 0.001 PHE A 212 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8128) covalent geometry : angle 0.58936 (11013) SS BOND : bond 0.00457 ( 3) SS BOND : angle 2.57138 ( 6) hydrogen bonds : bond 0.03856 ( 401) hydrogen bonds : angle 4.09041 ( 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 160 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8273 (mm110) cc_final: 0.7896 (pt0) REVERT: A 13 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7620 (mtm-85) REVERT: A 38 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8387 (mmt90) REVERT: A 216 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8963 (mmpt) REVERT: B 10 GLU cc_start: 0.8645 (tp30) cc_final: 0.8119 (tp30) REVERT: B 15 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8741 (mmmm) REVERT: B 127 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8741 (ptpt) REVERT: B 215 GLU cc_start: 0.8825 (pm20) cc_final: 0.8200 (pm20) REVERT: B 217 MET cc_start: 0.7448 (pmt) cc_final: 0.6747 (pmt) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7598 (t80) REVERT: B 256 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7460 (ptt-90) REVERT: G 47 GLU cc_start: 0.8724 (pm20) cc_final: 0.8458 (pm20) REVERT: R 646 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7190 (tm-30) REVERT: R 768 ASP cc_start: 0.5375 (p0) cc_final: 0.4784 (m-30) REVERT: R 822 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8086 (tm-30) REVERT: R 862 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8095 (pp) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 0.5967 time to fit residues: 95.3759 Evaluate side-chains 153 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 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 11 LEU 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 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: 5.9990 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 881 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.093114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.069384 restraints weight = 14474.133| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.85 r_work: 0.2871 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1952 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= 0.161 Angle : 0.620 7.390 11019 Z= 0.330 Chirality : 0.043 0.146 1243 Planarity : 0.004 0.055 1394 Dihedral : 4.327 34.860 1153 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.42 % Allowed : 23.47 % 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: 0.79 (0.27), residues: 988 helix: 2.36 (0.26), residues: 375 sheet: 0.02 (0.34), residues: 223 loop : -1.02 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 105 TYR 0.013 0.001 TYR A 339 PHE 0.010 0.001 PHE R 634 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8128) covalent geometry : angle 0.61661 (11013) SS BOND : bond 0.00500 ( 3) SS BOND : angle 2.80310 ( 6) hydrogen bonds : bond 0.04121 ( 401) hydrogen bonds : angle 4.22399 ( 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 159 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8273 (mm110) cc_final: 0.7869 (pt0) REVERT: A 13 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7701 (mtm-85) REVERT: A 38 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8364 (mmt90) REVERT: A 216 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8968 (mmpt) REVERT: B 10 GLU cc_start: 0.8671 (tp30) cc_final: 0.8157 (tp30) REVERT: B 15 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8734 (mmmm) REVERT: B 127 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8729 (ptpt) REVERT: B 215 GLU cc_start: 0.8914 (pm20) cc_final: 0.8694 (pm20) REVERT: B 234 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.7599 (t80) REVERT: B 256 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7541 (ptt-90) REVERT: G 20 LYS cc_start: 0.8237 (pttm) cc_final: 0.8029 (pttm) REVERT: G 47 GLU cc_start: 0.8764 (pm20) cc_final: 0.8487 (pm20) REVERT: R 646 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7127 (tm-30) REVERT: R 822 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8087 (tm-30) REVERT: R 862 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8065 (pp) outliers start: 29 outliers final: 17 residues processed: 152 average time/residue: 0.5999 time to fit residues: 96.2444 Evaluate side-chains 145 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 274 ASP 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 96 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 881 GLN ** 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 = 0.3417 r_free = 0.3417 target = 0.093078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.069436 restraints weight = 14440.621| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.84 r_work: 0.2875 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1998 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= 0.154 Angle : 0.626 7.634 11019 Z= 0.332 Chirality : 0.043 0.144 1243 Planarity : 0.004 0.060 1394 Dihedral : 4.324 34.667 1153 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 24.29 % 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: 0.78 (0.27), residues: 988 helix: 2.35 (0.26), residues: 375 sheet: 0.01 (0.34), residues: 223 loop : -1.01 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.011 0.001 TYR A 339 PHE 0.010 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8128) covalent geometry : angle 0.62260 (11013) SS BOND : bond 0.00469 ( 3) SS BOND : angle 2.65475 ( 6) hydrogen bonds : bond 0.04062 ( 401) hydrogen bonds : angle 4.22804 ( 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 149 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8250 (mm110) cc_final: 0.7929 (pt0) REVERT: A 38 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8354 (mmt90) REVERT: A 216 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8956 (mmpt) REVERT: B 10 GLU cc_start: 0.8671 (tp30) cc_final: 0.8191 (tp30) REVERT: B 15 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8731 (mmmm) REVERT: B 127 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8730 (ptpt) REVERT: B 234 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.7587 (t80) REVERT: G 47 GLU cc_start: 0.8765 (pm20) cc_final: 0.8551 (pm20) REVERT: R 711 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8800 (mtp) REVERT: R 822 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8083 (tm-30) REVERT: R 862 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8058 (pp) outliers start: 25 outliers final: 14 residues processed: 145 average time/residue: 0.6553 time to fit residues: 100.1126 Evaluate side-chains 149 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** R 881 GLN ** 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 = 0.3407 r_free = 0.3407 target = 0.092424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.068696 restraints weight = 14475.504| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.86 r_work: 0.2847 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1989 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= 0.178 Angle : 0.643 7.561 11019 Z= 0.341 Chirality : 0.044 0.148 1243 Planarity : 0.004 0.059 1394 Dihedral : 4.428 35.729 1153 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.83 % Allowed : 24.17 % 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: 0.74 (0.27), residues: 988 helix: 2.28 (0.26), residues: 375 sheet: 0.00 (0.34), residues: 223 loop : -1.01 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.013 0.001 TYR A 339 PHE 0.011 0.001 PHE R 634 TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8128) covalent geometry : angle 0.63980 (11013) SS BOND : bond 0.00485 ( 3) SS BOND : angle 2.84961 ( 6) hydrogen bonds : bond 0.04253 ( 401) hydrogen bonds : angle 4.29052 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.51 seconds wall clock time: 55 minutes 37.51 seconds (3337.51 seconds total)