Starting phenix.real_space_refine on Wed Mar 4 09:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.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 { model { file = "/net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkf_33250/03_2026/7xkf_33250.map" } 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 1454 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7961 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AND': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.28 Number of scatterers: 7961 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 1454 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: 0.68 Conformation dependent library (CDL) restraints added in 311.0 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: 0.16 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: 1.06 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 1.680 -0.348 2.00e-02 2.50e+03 3.02e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.740 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.680 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.661 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.638 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 10659 1.55 - 3.09: 258 3.09 - 4.64: 59 4.64 - 6.18: 29 6.18 - 7.73: 8 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: 4249 17.29 - 34.57: 460 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 - 0.069: 1093 0.069 - 0.139: 145 0.139 - 0.208: 3 0.208 - 0.277: 1 0.277 - 0.346: 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 -2.37 -0.35 2.00e-01 2.50e+01 3.00e+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 -2.73 0.27 2.00e-01 2.50e+01 1.80e+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: 2.06 - 2.62: 118 2.62 - 3.19: 7185 3.19 - 3.76: 12363 3.76 - 4.33: 17452 4.33 - 4.90: 29049 Nonbonded interactions: 66167 Sorted by model distance: 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 nonbonded pdb=" O SER A 251 " pdb=" NZ LYS A 300 " model vdw 2.222 3.120 ... (remaining 66162 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: 1.680 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 0.348 8131 Z= 0.330 Angle : 0.679 7.729 11019 Z= 0.378 Chirality : 0.046 0.346 1243 Planarity : 0.006 0.112 1394 Dihedral : 15.092 85.281 2945 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.06 % Allowed : 17.22 % Favored : 81.72 % 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 0.00684 ( 8128) covalent geometry : angle 0.67844 (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: 9 poor density : 159 time to evaluate : 0.309 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: 9 outliers final: 7 residues processed: 166 average time/residue: 0.6785 time to fit residues: 117.8630 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 : 0.273 ------------------------------------------------------------------------------- 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 = 0.091051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.067205 restraints weight = 14512.415| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.90 r_work: 0.2787 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1198 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= 0.166 Angle : 0.576 6.860 11019 Z= 0.312 Chirality : 0.043 0.146 1243 Planarity : 0.004 0.067 1394 Dihedral : 5.100 46.345 1163 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.42 % Allowed : 20.17 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 988 helix: 2.53 (0.26), residues: 373 sheet: 0.07 (0.34), residues: 220 loop : -1.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 650 TYR 0.017 0.001 TYR A 339 PHE 0.019 0.001 PHE R 671 TRP 0.014 0.001 TRP B 211 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8128) covalent geometry : angle 0.57053 (11013) SS BOND : bond 0.00750 ( 3) SS BOND : angle 3.54416 ( 6) hydrogen bonds : bond 0.04655 ( 401) hydrogen bonds : angle 4.39460 ( 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 166 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.338 Fit side-chains REVERT: A 12 GLN cc_start: 0.8269 (mm110) cc_final: 0.7852 (pt0) REVERT: A 38 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8400 (mmt90) REVERT: A 216 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8879 (mmpt) REVERT: A 220 HIS cc_start: 0.8697 (m170) cc_final: 0.8442 (m170) REVERT: A 296 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 381 ASP cc_start: 0.9004 (t70) cc_final: 0.8612 (t70) REVERT: B 23 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8639 (tppt) REVERT: B 61 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9090 (ppp) REVERT: G 13 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8179 (mtm110) REVERT: G 47 GLU cc_start: 0.8747 (pm20) cc_final: 0.8480 (pm20) REVERT: G 58 GLU cc_start: 0.8291 (pm20) cc_final: 0.8055 (pm20) REVERT: R 646 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 29 outliers final: 8 residues processed: 153 average time/residue: 0.6120 time to fit residues: 98.6812 Evaluate side-chains 140 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 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 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 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 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3376 r_free = 0.3376 target = 0.091433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067740 restraints weight = 14413.965| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.91 r_work: 0.2790 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8131 Z= 0.144 Angle : 0.545 6.102 11019 Z= 0.293 Chirality : 0.042 0.149 1243 Planarity : 0.004 0.056 1394 Dihedral : 4.383 36.914 1153 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.01 % Allowed : 19.93 % 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: 0.89 (0.27), residues: 988 helix: 2.56 (0.26), residues: 373 sheet: 0.01 (0.33), residues: 221 loop : -1.04 (0.30), residues: 394 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 0.015 0.001 PHE R 671 TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8128) covalent geometry : angle 0.54098 (11013) SS BOND : bond 0.00465 ( 3) SS BOND : angle 2.76368 ( 6) hydrogen bonds : bond 0.04236 ( 401) hydrogen bonds : angle 4.25373 ( 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 173 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.215 Fit side-chains REVERT: A 12 GLN cc_start: 0.8339 (mm110) cc_final: 0.7847 (pt0) REVERT: A 38 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (mmt90) REVERT: A 216 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8917 (mmpt) REVERT: A 296 LEU cc_start: 0.8632 (mt) cc_final: 0.8394 (mp) REVERT: B 10 GLU cc_start: 0.8560 (tp30) cc_final: 0.8299 (tp30) REVERT: B 23 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8627 (tppt) REVERT: B 61 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9105 (ppp) REVERT: B 234 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.7559 (t80) REVERT: G 13 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8199 (mtm110) REVERT: G 47 GLU cc_start: 0.8723 (pm20) cc_final: 0.8494 (pm20) REVERT: N 3 GLN cc_start: 0.8419 (tt0) cc_final: 0.8199 (tt0) REVERT: R 646 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7305 (tm-30) outliers start: 34 outliers final: 13 residues processed: 165 average time/residue: 0.6199 time to fit residues: 107.6960 Evaluate side-chains 139 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 276 VAL 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 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 41 optimal weight: 0.0570 chunk 72 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 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 = 0.3386 r_free = 0.3386 target = 0.092430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.068734 restraints weight = 14636.007| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.94 r_work: 0.2820 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8131 Z= 0.118 Angle : 0.538 7.638 11019 Z= 0.287 Chirality : 0.041 0.141 1243 Planarity : 0.004 0.052 1394 Dihedral : 4.241 34.402 1153 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.54 % Allowed : 21.46 % Favored : 75.00 % 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: 0.90 (0.27), residues: 988 helix: 2.56 (0.26), residues: 375 sheet: 0.03 (0.34), residues: 221 loop : -1.05 (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 0.012 0.001 PHE R 671 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8128) covalent geometry : angle 0.53511 (11013) SS BOND : bond 0.00341 ( 3) SS BOND : angle 2.27647 ( 6) hydrogen bonds : bond 0.03906 ( 401) hydrogen bonds : angle 4.15737 ( 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 163 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.316 Fit side-chains REVERT: A 12 GLN cc_start: 0.8300 (mm110) cc_final: 0.7828 (pt0) REVERT: A 38 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8331 (mmt90) REVERT: A 216 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8943 (mmpt) REVERT: B 10 GLU cc_start: 0.8622 (tp30) cc_final: 0.8227 (tp30) REVERT: B 19 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8707 (ttp80) REVERT: B 23 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8638 (tppt) REVERT: B 234 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.7651 (t80) REVERT: B 256 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7449 (ptt-90) REVERT: G 47 GLU cc_start: 0.8698 (pm20) cc_final: 0.8400 (pm20) REVERT: G 58 GLU cc_start: 0.8235 (pm20) cc_final: 0.8030 (pm20) REVERT: N 3 GLN cc_start: 0.8413 (tt0) cc_final: 0.8193 (tt0) REVERT: R 646 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7252 (tm-30) REVERT: R 650 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8241 (mmt90) outliers start: 30 outliers final: 15 residues processed: 154 average time/residue: 0.6754 time to fit residues: 109.0840 Evaluate side-chains 149 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3388 r_free = 0.3388 target = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.068556 restraints weight = 14451.717| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.90 r_work: 0.2806 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8131 Z= 0.136 Angle : 0.558 6.496 11019 Z= 0.297 Chirality : 0.042 0.143 1243 Planarity : 0.004 0.049 1394 Dihedral : 4.232 34.569 1153 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.13 % Allowed : 22.05 % Favored : 73.82 % 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: 0.87 (0.27), residues: 988 helix: 2.49 (0.26), residues: 375 sheet: 0.05 (0.34), residues: 221 loop : -1.03 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 13 TYR 0.010 0.001 TYR A 339 PHE 0.011 0.001 PHE R 856 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8128) covalent geometry : angle 0.55522 (11013) SS BOND : bond 0.00407 ( 3) SS BOND : angle 2.46090 ( 6) hydrogen bonds : bond 0.04009 ( 401) hydrogen bonds : angle 4.14833 ( 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 171 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.265 Fit side-chains REVERT: A 12 GLN cc_start: 0.8251 (mm110) cc_final: 0.7851 (pt0) REVERT: A 38 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8353 (mmt90) REVERT: A 216 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8955 (mmpt) REVERT: B 10 GLU cc_start: 0.8628 (tp30) cc_final: 0.8205 (tp30) REVERT: B 19 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8716 (ttp80) REVERT: B 23 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8666 (tppt) REVERT: B 127 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8710 (ptpt) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7563 (t80) REVERT: B 256 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7584 (ptt-90) REVERT: B 325 MET cc_start: 0.9107 (mmt) cc_final: 0.8877 (mmm) REVERT: G 47 GLU cc_start: 0.8699 (pm20) cc_final: 0.8411 (pm20) REVERT: N 3 GLN cc_start: 0.8414 (tt0) cc_final: 0.8194 (tt0) REVERT: R 646 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7240 (tm-30) REVERT: R 862 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7923 (pp) outliers start: 35 outliers final: 14 residues processed: 162 average time/residue: 0.6243 time to fit residues: 106.3464 Evaluate side-chains 142 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.068232 restraints weight = 14392.417| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.92 r_work: 0.2807 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1811 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= 0.140 Angle : 0.576 7.558 11019 Z= 0.304 Chirality : 0.042 0.141 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.227 34.300 1153 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.89 % Allowed : 22.76 % Favored : 73.35 % 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: 0.85 (0.27), residues: 988 helix: 2.45 (0.26), residues: 375 sheet: 0.07 (0.34), residues: 221 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 13 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE R 856 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8128) covalent geometry : angle 0.57298 (11013) SS BOND : bond 0.00330 ( 3) SS BOND : angle 2.39630 ( 6) hydrogen bonds : bond 0.04010 ( 401) hydrogen bonds : angle 4.18274 ( 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 159 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8282 (mm110) cc_final: 0.7863 (pt0) REVERT: A 38 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8342 (mmt90) REVERT: A 216 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8989 (mmpt) REVERT: B 10 GLU cc_start: 0.8651 (tp30) cc_final: 0.8179 (tp30) REVERT: B 19 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8706 (ttp80) REVERT: B 23 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8707 (tppt) REVERT: B 127 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8703 (ptpt) REVERT: B 234 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.7486 (t80) REVERT: B 256 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7557 (ptt-90) REVERT: B 325 MET cc_start: 0.9102 (mmt) cc_final: 0.8877 (mmm) REVERT: G 20 LYS cc_start: 0.8309 (pttm) cc_final: 0.8086 (pttm) REVERT: G 47 GLU cc_start: 0.8731 (pm20) cc_final: 0.8455 (pm20) REVERT: R 646 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7210 (tm-30) REVERT: R 650 ARG cc_start: 0.8519 (mmt90) cc_final: 0.8309 (mmt90) REVERT: R 822 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8074 (tm-30) REVERT: R 862 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7931 (pp) outliers start: 33 outliers final: 17 residues processed: 152 average time/residue: 0.6538 time to fit residues: 104.5154 Evaluate side-chains 152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 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 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 85 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068269 restraints weight = 14573.092| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.93 r_work: 0.2809 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1861 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= 0.138 Angle : 0.579 7.773 11019 Z= 0.307 Chirality : 0.042 0.139 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.232 34.065 1153 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.66 % Allowed : 23.00 % Favored : 73.35 % 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: 0.83 (0.27), residues: 988 helix: 2.43 (0.26), residues: 375 sheet: 0.04 (0.34), residues: 221 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 13 TYR 0.011 0.001 TYR N 60 PHE 0.012 0.001 PHE R 856 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8128) covalent geometry : angle 0.57589 (11013) SS BOND : bond 0.00558 ( 3) SS BOND : angle 2.58823 ( 6) hydrogen bonds : bond 0.03985 ( 401) hydrogen bonds : angle 4.15754 ( 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 165 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.322 Fit side-chains REVERT: A 12 GLN cc_start: 0.8209 (mm110) cc_final: 0.7823 (pt0) REVERT: A 13 ARG cc_start: 0.8297 (mpt180) cc_final: 0.7750 (mtm-85) REVERT: A 38 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (mmt90) REVERT: A 216 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8987 (mmpt) REVERT: B 10 GLU cc_start: 0.8665 (tp30) cc_final: 0.8179 (tp30) REVERT: B 23 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8715 (tppt) REVERT: B 127 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8704 (ptpt) REVERT: B 215 GLU cc_start: 0.8864 (pm20) cc_final: 0.8229 (pm20) REVERT: B 217 MET cc_start: 0.7486 (pmt) cc_final: 0.6752 (pmt) REVERT: B 234 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.7483 (t80) REVERT: B 325 MET cc_start: 0.9087 (mmt) cc_final: 0.8859 (mmm) REVERT: G 20 LYS cc_start: 0.8261 (pttm) cc_final: 0.8037 (pttm) REVERT: G 47 GLU cc_start: 0.8736 (pm20) cc_final: 0.8449 (pm20) REVERT: R 646 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7130 (tm-30) REVERT: R 650 ARG cc_start: 0.8544 (mmt90) cc_final: 0.8290 (mmt90) REVERT: R 768 ASP cc_start: 0.5520 (p0) cc_final: 0.4895 (m-30) REVERT: R 822 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8068 (tm-30) REVERT: R 862 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7919 (pp) outliers start: 31 outliers final: 17 residues processed: 156 average time/residue: 0.6558 time to fit residues: 107.4930 Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 3 GLU 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 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 8 optimal weight: 0.0870 chunk 48 optimal weight: 0.0470 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3421 r_free = 0.3421 target = 0.094227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070212 restraints weight = 14550.095| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.93 r_work: 0.2852 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8131 Z= 0.116 Angle : 0.580 8.623 11019 Z= 0.308 Chirality : 0.041 0.140 1243 Planarity : 0.004 0.054 1394 Dihedral : 4.127 32.186 1153 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.18 % Allowed : 23.82 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 988 helix: 2.46 (0.26), residues: 369 sheet: 0.10 (0.34), residues: 220 loop : -0.92 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 13 TYR 0.011 0.001 TYR N 60 PHE 0.012 0.001 PHE R 856 TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8128) covalent geometry : angle 0.57824 (11013) SS BOND : bond 0.00370 ( 3) SS BOND : angle 2.18517 ( 6) hydrogen bonds : bond 0.03705 ( 401) hydrogen bonds : angle 4.14309 ( 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 156 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.258 Fit side-chains REVERT: A 12 GLN cc_start: 0.8206 (mm110) cc_final: 0.7927 (pt0) REVERT: A 38 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8309 (mmt90) REVERT: A 216 LYS cc_start: 0.9216 (mtmm) cc_final: 0.8981 (mmpt) REVERT: B 10 GLU cc_start: 0.8663 (tp30) cc_final: 0.8164 (tp30) REVERT: B 127 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8632 (ptpt) REVERT: B 234 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 325 MET cc_start: 0.9080 (mmt) cc_final: 0.8844 (mmm) REVERT: G 47 GLU cc_start: 0.8746 (pm20) cc_final: 0.8484 (pm20) REVERT: R 646 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7025 (tm-30) REVERT: R 650 ARG cc_start: 0.8467 (mmt90) cc_final: 0.8262 (mmt90) REVERT: R 803 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: R 822 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8052 (tm-30) REVERT: R 862 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7901 (pp) outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 0.6118 time to fit residues: 94.6969 Evaluate side-chains 150 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 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 803 GLN 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 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** B 155 ASN N 123 GLN ** 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 = 0.3391 r_free = 0.3391 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.068711 restraints weight = 14443.052| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.88 r_work: 0.2813 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8131 Z= 0.147 Angle : 0.611 7.416 11019 Z= 0.323 Chirality : 0.043 0.145 1243 Planarity : 0.004 0.056 1394 Dihedral : 4.218 33.608 1153 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.42 % Allowed : 23.94 % Favored : 72.64 % 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: 0.77 (0.27), residues: 988 helix: 2.30 (0.26), residues: 375 sheet: 0.06 (0.34), residues: 221 loop : -1.00 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.012 0.001 TYR N 60 PHE 0.012 0.001 PHE R 856 TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8128) covalent geometry : angle 0.60756 (11013) SS BOND : bond 0.00469 ( 3) SS BOND : angle 2.63628 ( 6) hydrogen bonds : bond 0.04009 ( 401) hydrogen bonds : angle 4.21257 ( 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 163 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.215 Fit side-chains REVERT: A 12 GLN cc_start: 0.8142 (mm110) cc_final: 0.7828 (pt0) REVERT: A 13 ARG cc_start: 0.8300 (mpt180) cc_final: 0.8077 (mtm-85) REVERT: A 38 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (mmt90) REVERT: A 216 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8993 (mmpt) REVERT: B 10 GLU cc_start: 0.8636 (tp30) cc_final: 0.8140 (tp30) REVERT: B 127 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8696 (ptpt) REVERT: B 234 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 325 MET cc_start: 0.9095 (mmt) cc_final: 0.8872 (mmm) REVERT: G 47 GLU cc_start: 0.8741 (pm20) cc_final: 0.8453 (pm20) REVERT: R 646 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7034 (tm-30) REVERT: R 650 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8276 (mmt90) REVERT: R 711 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8778 (mtp) REVERT: R 822 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8071 (tm-30) REVERT: R 862 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7940 (pp) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 0.6083 time to fit residues: 100.6638 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 : 0.223 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** B 155 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 = 0.3410 r_free = 0.3410 target = 0.093564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069928 restraints weight = 14294.499| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.88 r_work: 0.2837 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8131 Z= 0.131 Angle : 0.622 7.897 11019 Z= 0.330 Chirality : 0.042 0.151 1243 Planarity : 0.004 0.061 1394 Dihedral : 4.183 32.675 1153 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.71 % Allowed : 24.65 % Favored : 72.64 % 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: 2.27 (0.26), residues: 376 sheet: 0.10 (0.34), residues: 220 loop : -1.00 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.011 0.001 TYR N 60 PHE 0.012 0.001 PHE R 856 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8128) covalent geometry : angle 0.61974 (11013) SS BOND : bond 0.00326 ( 3) SS BOND : angle 2.24634 ( 6) hydrogen bonds : bond 0.03831 ( 401) hydrogen bonds : angle 4.18280 ( 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: 23 poor density : 126 time to evaluate : 0.294 Fit side-chains REVERT: A 12 GLN cc_start: 0.8167 (mm110) cc_final: 0.7925 (pt0) REVERT: A 13 ARG cc_start: 0.8261 (mpt180) cc_final: 0.8012 (mtm-85) REVERT: A 38 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8302 (mmt90) REVERT: A 216 LYS cc_start: 0.9209 (mtmm) cc_final: 0.8977 (mmpt) REVERT: B 10 GLU cc_start: 0.8672 (tp30) cc_final: 0.8218 (tp30) REVERT: B 15 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8716 (mmmm) REVERT: B 127 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8612 (ptpt) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.7520 (t80) REVERT: G 13 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8162 (mtm110) REVERT: G 47 GLU cc_start: 0.8739 (pm20) cc_final: 0.8441 (pm20) REVERT: R 646 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6976 (tm-30) REVERT: R 650 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8273 (mmt90) REVERT: R 711 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: R 822 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8057 (tm-30) REVERT: R 862 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7927 (pp) outliers start: 23 outliers final: 14 residues processed: 143 average time/residue: 0.6355 time to fit residues: 95.6358 Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 4 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 31 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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** B 155 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 = 0.3409 r_free = 0.3409 target = 0.093506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069856 restraints weight = 14400.197| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.89 r_work: 0.2836 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8131 Z= 0.131 Angle : 0.619 8.036 11019 Z= 0.328 Chirality : 0.042 0.162 1243 Planarity : 0.004 0.059 1394 Dihedral : 4.171 32.505 1153 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.59 % Allowed : 25.12 % Favored : 72.29 % 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: 0.77 (0.27), residues: 988 helix: 2.28 (0.27), residues: 376 sheet: 0.09 (0.34), residues: 220 loop : -1.00 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.011 0.001 TYR N 60 PHE 0.012 0.001 PHE R 856 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8128) covalent geometry : angle 0.61673 (11013) SS BOND : bond 0.00347 ( 3) SS BOND : angle 2.27298 ( 6) hydrogen bonds : bond 0.03817 ( 401) hydrogen bonds : angle 4.16596 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3221.70 seconds wall clock time: 55 minutes 25.61 seconds (3325.61 seconds total)