Starting phenix.real_space_refine on Thu Jul 2 06:25:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjk_17712/07_2026/8pjk_17712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjk_17712/07_2026/8pjk_17712.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/8pjk_17712/07_2026/8pjk_17712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjk_17712/07_2026/8pjk_17712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pjk_17712/07_2026/8pjk_17712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjk_17712/07_2026/8pjk_17712.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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 4583 2.51 5 N 1215 2.21 5 O 1373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1790 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2256 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Chain: "R" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'CLR': 2, 'T7M': 1, 'ZL9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 1.50, per 1000 atoms: 0.21 Number of scatterers: 7227 At special positions: 0 Unit cell: (76.4992, 100.878, 125.257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 2 15.00 O 1373 8.00 N 1215 7.00 C 4583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 0.60 Conformation dependent library (CDL) restraints added in 269.2 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 49.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.708A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.310A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.096A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.106A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.893A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.544A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 35 through 64 Processing helix chain 'R' and resid 65 through 68 Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.443A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 174 removed outlier: 3.829A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 230 removed outlier: 4.033A pdb=" N THR R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL R 230 " --> pdb=" O ILE R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.602A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 378 through 391 Processing helix chain 'R' and resid 391 through 402 Proline residue: R 397 - end of helix removed outlier: 3.640A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.649A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.348A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.666A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.887A 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: 6.917A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.639A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.837A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.679A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.821A 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: 3.876A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1209 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: 1.07 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1254 1.32 - 1.45: 1870 1.45 - 1.57: 4127 1.57 - 1.69: 3 1.69 - 1.81: 76 Bond restraints: 7330 Sorted by residual: bond pdb=" O4 T7M R 504 " pdb=" P4 T7M R 504 " ideal model delta sigma weight residual 1.704 1.626 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O13 T7M R 504 " pdb=" P1 T7M R 504 " ideal model delta sigma weight residual 1.659 1.599 0.060 2.00e-02 2.50e+03 9.09e+00 bond pdb=" C11 ZL9 R 503 " pdb=" N12 ZL9 R 503 " ideal model delta sigma weight residual 1.448 1.493 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C4 T7M R 504 " pdb=" O4 T7M R 504 " ideal model delta sigma weight residual 1.402 1.443 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" O41 T7M R 504 " pdb=" P4 T7M R 504 " ideal model delta sigma weight residual 1.554 1.515 0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 7325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 9608 1.29 - 2.58: 257 2.58 - 3.86: 50 3.86 - 5.15: 18 5.15 - 6.44: 6 Bond angle restraints: 9939 Sorted by residual: angle pdb=" N ILE R 169 " pdb=" CA ILE R 169 " pdb=" C ILE R 169 " ideal model delta sigma weight residual 108.88 115.01 -6.13 2.16e+00 2.14e-01 8.05e+00 angle pdb=" C GLU A 238 " pdb=" N GLU A 239 " pdb=" CA GLU A 239 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.14e+00 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 113.33 -2.63 1.22e+00 6.72e-01 4.66e+00 angle pdb=" O1 T7M R 504 " pdb=" P1 T7M R 504 " pdb=" O12 T7M R 504 " ideal model delta sigma weight residual 105.26 111.70 -6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" C GLN B 156 " pdb=" N ILE B 157 " pdb=" CA ILE B 157 " ideal model delta sigma weight residual 122.71 119.77 2.94 1.44e+00 4.82e-01 4.18e+00 ... (remaining 9934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 4438 32.82 - 65.65: 57 65.65 - 98.47: 12 98.47 - 131.30: 4 131.30 - 164.12: 2 Dihedral angle restraints: 4513 sinusoidal: 1885 harmonic: 2628 Sorted by residual: dihedral pdb=" C10 T7M R 504 " pdb=" C8 T7M R 504 " pdb=" O16 T7M R 504 " pdb=" C7 T7M R 504 " ideal model delta sinusoidal sigma weight residual 55.77 -108.35 164.12 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C10 T7M R 504 " pdb=" C8 T7M R 504 " pdb=" O16 T7M R 504 " pdb=" C9 T7M R 504 " ideal model delta sinusoidal sigma weight residual 288.02 130.62 157.40 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C4 T7M R 504 " pdb=" C5 T7M R 504 " pdb=" C6 T7M R 504 " pdb=" O6 T7M R 504 " ideal model delta sinusoidal sigma weight residual 293.67 170.94 122.73 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 984 0.060 - 0.120: 156 0.120 - 0.179: 7 0.179 - 0.239: 0 0.239 - 0.299: 1 Chirality restraints: 1148 Sorted by residual: chirality pdb=" C8 T7M R 504 " pdb=" C7 T7M R 504 " pdb=" C9 T7M R 504 " pdb=" O16 T7M R 504 " both_signs ideal model delta sigma weight residual False -2.26 -2.56 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1145 not shown) Planarity restraints: 1237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 ZL9 R 503 " -0.019 2.00e-02 2.50e+03 6.66e-02 5.55e+01 pdb=" C23 ZL9 R 503 " -0.017 2.00e-02 2.50e+03 pdb=" C26 ZL9 R 503 " 0.080 2.00e-02 2.50e+03 pdb=" N24 ZL9 R 503 " -0.107 2.00e-02 2.50e+03 pdb=" O25 ZL9 R 503 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 ZL9 R 503 " -0.013 2.00e-02 2.50e+03 1.26e-02 3.56e+00 pdb=" C18 ZL9 R 503 " -0.009 2.00e-02 2.50e+03 pdb=" C19 ZL9 R 503 " -0.004 2.00e-02 2.50e+03 pdb=" C20 ZL9 R 503 " -0.001 2.00e-02 2.50e+03 pdb=" C26 ZL9 R 503 " -0.005 2.00e-02 2.50e+03 pdb=" C27 ZL9 R 503 " -0.012 2.00e-02 2.50e+03 pdb=" N24 ZL9 R 503 " 0.002 2.00e-02 2.50e+03 pdb=" O16 ZL9 R 503 " 0.026 2.00e-02 2.50e+03 pdb=" O21 ZL9 R 503 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 ZL9 R 503 " -0.017 2.00e-02 2.50e+03 1.07e-02 2.29e+00 pdb=" C04 ZL9 R 503 " -0.006 2.00e-02 2.50e+03 pdb=" C05 ZL9 R 503 " 0.007 2.00e-02 2.50e+03 pdb=" C06 ZL9 R 503 " 0.009 2.00e-02 2.50e+03 pdb=" C07 ZL9 R 503 " -0.002 2.00e-02 2.50e+03 pdb=" C08 ZL9 R 503 " -0.014 2.00e-02 2.50e+03 pdb=" O02 ZL9 R 503 " 0.015 2.00e-02 2.50e+03 pdb=" O09 ZL9 R 503 " 0.008 2.00e-02 2.50e+03 ... (remaining 1234 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1150 2.76 - 3.30: 6956 3.30 - 3.83: 12514 3.83 - 4.37: 15083 4.37 - 4.90: 25754 Nonbonded interactions: 61457 Sorted by model distance: nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.225 3.120 nonbonded pdb=" OG SER R 123 " pdb=" O HOH R 601 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP R 82 " pdb=" O HOH R 602 " model vdw 2.255 3.040 nonbonded pdb=" O ASP R 133 " pdb=" O HOH R 603 " model vdw 2.262 3.040 nonbonded pdb=" O HOH A 402 " pdb=" O HOH R 630 " model vdw 2.283 3.040 ... (remaining 61452 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7331 Z= 0.165 Angle : 0.561 6.441 9941 Z= 0.296 Chirality : 0.042 0.299 1148 Planarity : 0.004 0.067 1237 Dihedral : 13.458 164.121 2804 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 888 helix: 2.41 (0.26), residues: 417 sheet: 0.59 (0.37), residues: 175 loop : -1.01 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR R 198 PHE 0.018 0.002 PHE B 151 TRP 0.015 0.002 TRP B 339 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 ( 7330) covalent geometry : angle 0.56146 / 0.30 ( 9939) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.09950 / 0.06 ( 2) hydrogen bonds : bond 0.05234 / 3.85 ( 422) hydrogen bonds : angle 4.39787 / 3.05 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: B 16 ASN cc_start: 0.6862 (t0) cc_final: 0.6636 (t0) REVERT: G 29 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7583 (mmtm) REVERT: R 334 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7794 (mmmm) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.5125 time to fit residues: 75.4774 Evaluate side-chains 106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN R 328 ASN R 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119295 restraints weight = 7973.828| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.68 r_work: 0.3315 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7331 Z= 0.119 Angle : 0.535 8.300 9941 Z= 0.277 Chirality : 0.041 0.158 1148 Planarity : 0.004 0.032 1237 Dihedral : 9.700 109.615 1172 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.69 % Allowed : 10.29 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.28), residues: 888 helix: 2.68 (0.26), residues: 406 sheet: 0.65 (0.37), residues: 174 loop : -0.83 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 227 TYR 0.011 0.001 TYR R 198 PHE 0.017 0.001 PHE B 151 TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 7330) covalent geometry : angle 0.53508 / 0.28 ( 9939) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.04906 / 0.03 ( 2) hydrogen bonds : bond 0.03876 / 2.59 ( 422) hydrogen bonds : angle 4.21937 / 2.95 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: G 29 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7328 (mmtm) REVERT: G 50 LEU cc_start: 0.8389 (mt) cc_final: 0.7939 (mp) REVERT: R 223 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6666 (tmm160) REVERT: R 333 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7456 (ptp90) REVERT: R 334 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7852 (mmmm) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 0.5416 time to fit residues: 64.6061 Evaluate side-chains 106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115305 restraints weight = 7897.403| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.71 r_work: 0.3267 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7331 Z= 0.168 Angle : 0.573 6.619 9941 Z= 0.302 Chirality : 0.043 0.138 1148 Planarity : 0.004 0.035 1237 Dihedral : 8.074 106.480 1171 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.34 % Allowed : 11.33 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.28), residues: 888 helix: 2.52 (0.26), residues: 406 sheet: 0.67 (0.37), residues: 180 loop : -0.88 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.013 0.002 TYR R 198 PHE 0.025 0.002 PHE B 151 TRP 0.014 0.002 TRP R 387 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 7330) covalent geometry : angle 0.57301 / 0.30 ( 9939) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.15029 / 0.09 ( 2) hydrogen bonds : bond 0.04548 / 3.07 ( 422) hydrogen bonds : angle 4.46456 / 3.12 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: B 23 LYS cc_start: 0.7757 (tttm) cc_final: 0.7478 (tppt) REVERT: B 188 MET cc_start: 0.8892 (mmm) cc_final: 0.8565 (mmm) REVERT: B 220 GLN cc_start: 0.8751 (mt0) cc_final: 0.8517 (mt0) REVERT: R 151 ARG cc_start: 0.7441 (ttt180) cc_final: 0.6724 (tmt170) REVERT: R 223 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6858 (tmm160) REVERT: R 334 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7841 (mmmm) outliers start: 18 outliers final: 8 residues processed: 119 average time/residue: 0.6099 time to fit residues: 76.3666 Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN G 59 ASN R 328 ASN R 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117908 restraints weight = 7989.527| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.71 r_work: 0.3310 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7331 Z= 0.109 Angle : 0.498 6.025 9941 Z= 0.265 Chirality : 0.040 0.134 1148 Planarity : 0.003 0.031 1237 Dihedral : 7.557 98.352 1171 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 888 helix: 2.70 (0.26), residues: 406 sheet: 0.72 (0.37), residues: 174 loop : -0.85 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 227 TYR 0.011 0.001 TYR R 198 PHE 0.015 0.001 PHE B 151 TRP 0.013 0.001 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 7330) covalent geometry : angle 0.49843 / 0.26 ( 9939) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.09091 / 0.05 ( 2) hydrogen bonds : bond 0.03822 / 2.54 ( 422) hydrogen bonds : angle 4.20756 / 2.94 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7976 (ttp) cc_final: 0.7665 (tmm) REVERT: A 20 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: B 23 LYS cc_start: 0.7716 (tttm) cc_final: 0.7440 (tppt) REVERT: G 50 LEU cc_start: 0.8448 (mt) cc_final: 0.8218 (mp) REVERT: R 334 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7838 (mmmm) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.6182 time to fit residues: 74.8475 Evaluate side-chains 106 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 220 GLN R 328 ASN R 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117929 restraints weight = 7965.429| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.72 r_work: 0.3310 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7331 Z= 0.112 Angle : 0.505 6.108 9941 Z= 0.267 Chirality : 0.040 0.132 1148 Planarity : 0.003 0.031 1237 Dihedral : 7.390 91.089 1171 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.34 % Allowed : 12.89 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.28), residues: 888 helix: 2.72 (0.25), residues: 407 sheet: 0.73 (0.37), residues: 174 loop : -0.82 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 327 TYR 0.011 0.001 TYR R 195 PHE 0.016 0.001 PHE B 151 TRP 0.012 0.001 TRP R 387 HIS 0.002 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7330) covalent geometry : angle 0.50524 / 0.27 ( 9939) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.06938 / 0.04 ( 2) hydrogen bonds : bond 0.03808 / 2.53 ( 422) hydrogen bonds : angle 4.17898 / 2.92 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: G 50 LEU cc_start: 0.8416 (mt) cc_final: 0.8177 (mp) REVERT: R 223 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7592 (ttp-110) REVERT: R 334 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7793 (mmmm) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.6018 time to fit residues: 69.9260 Evaluate side-chains 109 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 333 ARG Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116767 restraints weight = 7988.401| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.71 r_work: 0.3291 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7331 Z= 0.141 Angle : 0.547 9.336 9941 Z= 0.288 Chirality : 0.042 0.133 1148 Planarity : 0.004 0.033 1237 Dihedral : 7.513 89.784 1171 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.47 % Allowed : 12.76 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.28), residues: 888 helix: 2.61 (0.26), residues: 406 sheet: 0.74 (0.37), residues: 175 loop : -0.80 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR R 195 PHE 0.020 0.002 PHE B 151 TRP 0.013 0.002 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7330) covalent geometry : angle 0.54752 / 0.29 ( 9939) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.04016 / 0.02 ( 2) hydrogen bonds : bond 0.04150 / 2.78 ( 422) hydrogen bonds : angle 4.30802 / 3.01 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: B 23 LYS cc_start: 0.7739 (tttm) cc_final: 0.7481 (tppt) REVERT: R 223 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7217 (ttp-110) REVERT: R 334 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7828 (mmmm) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.6156 time to fit residues: 73.9530 Evaluate side-chains 112 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 333 ARG Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.153591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118024 restraints weight = 7943.779| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.71 r_work: 0.3309 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7331 Z= 0.114 Angle : 0.536 13.668 9941 Z= 0.277 Chirality : 0.041 0.131 1148 Planarity : 0.003 0.032 1237 Dihedral : 7.296 84.242 1171 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.08 % Allowed : 13.80 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.28), residues: 888 helix: 2.68 (0.26), residues: 407 sheet: 0.75 (0.37), residues: 175 loop : -0.82 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 220 TYR 0.011 0.001 TYR R 195 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.001 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7330) covalent geometry : angle 0.53637 / 0.28 ( 9939) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.03596 / 0.02 ( 2) hydrogen bonds : bond 0.03864 / 2.57 ( 422) hydrogen bonds : angle 4.19919 / 2.93 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: B 23 LYS cc_start: 0.7697 (tttm) cc_final: 0.7445 (tppt) REVERT: R 334 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7806 (mmmm) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.6189 time to fit residues: 70.3758 Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN R 328 ASN R 404 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116776 restraints weight = 7984.905| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.70 r_work: 0.3291 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7331 Z= 0.142 Angle : 0.576 18.060 9941 Z= 0.296 Chirality : 0.042 0.181 1148 Planarity : 0.004 0.033 1237 Dihedral : 7.430 83.031 1171 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.95 % Allowed : 13.80 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.28), residues: 888 helix: 2.58 (0.25), residues: 407 sheet: 0.65 (0.37), residues: 181 loop : -0.76 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR R 195 PHE 0.021 0.002 PHE B 151 TRP 0.013 0.002 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7330) covalent geometry : angle 0.57599 / 0.30 ( 9939) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.15022 / 0.09 ( 2) hydrogen bonds : bond 0.04202 / 2.81 ( 422) hydrogen bonds : angle 4.32963 / 3.02 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: B 23 LYS cc_start: 0.7767 (tttm) cc_final: 0.7513 (tppt) REVERT: R 151 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6722 (tmt170) REVERT: R 334 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7838 (mmmm) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.6407 time to fit residues: 73.4679 Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118122 restraints weight = 7910.475| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.70 r_work: 0.3314 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7331 Z= 0.119 Angle : 0.523 9.578 9941 Z= 0.276 Chirality : 0.041 0.131 1148 Planarity : 0.004 0.032 1237 Dihedral : 7.210 76.574 1171 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 14.45 % Favored : 83.72 % 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: 1.71 (0.28), residues: 888 helix: 2.66 (0.25), residues: 407 sheet: 0.65 (0.36), residues: 180 loop : -0.74 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 220 TYR 0.012 0.001 TYR R 195 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.001 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7330) covalent geometry : angle 0.52297 / 0.28 ( 9939) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.07568 / 0.04 ( 2) hydrogen bonds : bond 0.03922 / 2.61 ( 422) hydrogen bonds : angle 4.19773 / 2.93 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: B 23 LYS cc_start: 0.7723 (tttm) cc_final: 0.7467 (tppt) REVERT: B 42 ARG cc_start: 0.6795 (tpp-160) cc_final: 0.6391 (tpt170) REVERT: R 334 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7818 (mmmm) outliers start: 14 outliers final: 11 residues processed: 110 average time/residue: 0.5913 time to fit residues: 68.6662 Evaluate side-chains 108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 36 optimal weight: 0.0170 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119421 restraints weight = 8005.977| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.70 r_work: 0.3330 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7331 Z= 0.105 Angle : 0.504 9.851 9941 Z= 0.266 Chirality : 0.040 0.134 1148 Planarity : 0.003 0.032 1237 Dihedral : 6.938 67.241 1171 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.43 % Allowed : 14.84 % Favored : 83.72 % 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: 1.79 (0.28), residues: 888 helix: 2.74 (0.25), residues: 407 sheet: 0.65 (0.36), residues: 185 loop : -0.70 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 220 TYR 0.011 0.001 TYR R 195 PHE 0.013 0.001 PHE B 151 TRP 0.013 0.001 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7330) covalent geometry : angle 0.50420 / 0.27 ( 9939) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.11501 / 0.07 ( 2) hydrogen bonds : bond 0.03671 / 2.43 ( 422) hydrogen bonds : angle 4.11073 / 2.88 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8021 (ttp) cc_final: 0.7677 (tmm) REVERT: A 29 LYS cc_start: 0.8008 (mppt) cc_final: 0.7669 (mmtm) REVERT: A 208 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7963 (ttp-110) REVERT: B 23 LYS cc_start: 0.7705 (tttm) cc_final: 0.7443 (tppt) REVERT: B 42 ARG cc_start: 0.6795 (tpp-160) cc_final: 0.6394 (tpt170) REVERT: G 50 LEU cc_start: 0.8317 (mt) cc_final: 0.7918 (mp) REVERT: R 334 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7794 (mmmm) outliers start: 11 outliers final: 11 residues processed: 110 average time/residue: 0.5976 time to fit residues: 69.3889 Evaluate side-chains 113 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 211 MET Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 328 ASN R 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118448 restraints weight = 7978.589| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.70 r_work: 0.3315 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7331 Z= 0.117 Angle : 0.530 9.810 9941 Z= 0.277 Chirality : 0.041 0.130 1148 Planarity : 0.004 0.032 1237 Dihedral : 6.976 69.496 1171 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.43 % Allowed : 15.36 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.28), residues: 888 helix: 2.70 (0.25), residues: 407 sheet: 0.76 (0.37), residues: 179 loop : -0.75 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 227 TYR 0.011 0.001 TYR R 195 PHE 0.016 0.001 PHE B 151 TRP 0.011 0.001 TRP R 387 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7330) covalent geometry : angle 0.52998 / 0.28 ( 9939) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.05786 / 0.03 ( 2) hydrogen bonds : bond 0.03864 / 2.57 ( 422) hydrogen bonds : angle 4.18106 / 2.92 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.81 seconds wall clock time: 58 minutes 30.07 seconds (3510.07 seconds total)