Starting phenix.real_space_refine on Fri Oct 23 20:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.cif Found real_map, /net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/44nx_82741/10_2026/44nx_82741.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.055 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6870 2.51 5 N 1871 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10951 Number of models: 1 Model: "" Number of chains: 7 Chain: "Q" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain breaks: 3 Chain: "U" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1029 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "W" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1029 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "X" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2365 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 14, 'TRANS': 289} Chain: "Y" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2310 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain: "B" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1014 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 2 Chain: "C" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1043 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Time building chain proxies: 2.18, per 1000 atoms: 0.20 Number of scatterers: 10951 At special positions: 0 Unit cell: (126.99, 104.58, 332, 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 38 16.00 O 2172 8.00 N 1871 7.00 C 6870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.85 Conformation dependent library (CDL) restraints added in 437.5 milliseconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 39.7% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'U' and resid 35 through 45 Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 72 through 76 removed outlier: 3.575A pdb=" N ASP U 75 " --> pdb=" O THR U 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 45 Processing helix chain 'W' and resid 72 through 76 Processing helix chain 'X' and resid 4 through 31 removed outlier: 3.675A pdb=" N ASN X 31 " --> pdb=" O ARG X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 59 removed outlier: 3.628A pdb=" N LEU X 59 " --> pdb=" O PHE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 84 Processing helix chain 'X' and resid 88 through 103 Proline residue: X 95 - end of helix Processing helix chain 'X' and resid 104 through 106 No H-bonds generated for 'chain 'X' and resid 104 through 106' Processing helix chain 'X' and resid 115 through 144 removed outlier: 3.903A pdb=" N GLU X 119 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 214 removed outlier: 3.837A pdb=" N LEU X 154 " --> pdb=" O PRO X 150 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL X 155 " --> pdb=" O PRO X 151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU X 193 " --> pdb=" O LYS X 189 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP X 208 " --> pdb=" O GLN X 204 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE X 209 " --> pdb=" O ALA X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 218 through 279 removed outlier: 3.879A pdb=" N GLU X 222 " --> pdb=" O ASN X 218 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL X 244 " --> pdb=" O ASN X 240 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU X 245 " --> pdb=" O TYR X 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET X 260 " --> pdb=" O ALA X 256 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER X 279 " --> pdb=" O ASN X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 279 through 301 removed outlier: 3.965A pdb=" N LEU X 283 " --> pdb=" O SER X 279 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN X 301 " --> pdb=" O ALA X 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 30 removed outlier: 3.545A pdb=" N ASN Y 30 " --> pdb=" O SER Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 55 through 60 Processing helix chain 'Y' and resid 64 through 84 Processing helix chain 'Y' and resid 93 through 105 removed outlier: 3.600A pdb=" N TRP Y 98 " --> pdb=" O LYS Y 94 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Y 99 " --> pdb=" O PRO Y 95 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 145 removed outlier: 3.741A pdb=" N PHE Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU Y 119 " --> pdb=" O VAL Y 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP Y 120 " --> pdb=" O PHE Y 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA Y 130 " --> pdb=" O ARG Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 215 removed outlier: 4.210A pdb=" N VAL Y 155 " --> pdb=" O PRO Y 151 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Y 156 " --> pdb=" O GLY Y 152 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP Y 215 " --> pdb=" O ARG Y 211 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 279 removed outlier: 3.896A pdb=" N LEU Y 221 " --> pdb=" O PRO Y 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG Y 225 " --> pdb=" O LEU Y 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER Y 236 " --> pdb=" O SER Y 232 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL Y 244 " --> pdb=" O ASN Y 240 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU Y 245 " --> pdb=" O TYR Y 241 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER Y 279 " --> pdb=" O ASN Y 275 " (cutoff:3.500A) Processing helix chain 'Y' and resid 279 through 296 removed outlier: 3.959A pdb=" N LEU Y 283 " --> pdb=" O SER Y 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.612A pdb=" N LEU C 22 " --> pdb=" O PRO C 18 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.795A pdb=" N TYR C 139 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU Q 365 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 375 through 379 removed outlier: 3.693A pdb=" N ASP Q 377 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 141 " --> pdb=" O ASP Q 377 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR B 139 " --> pdb=" O TRP Q 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 446 through 449 removed outlier: 3.511A pdb=" N LEU U 159 " --> pdb=" O ALA U 111 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA U 111 " --> pdb=" O LEU U 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 97 through 98 removed outlier: 3.757A pdb=" N ASP U 105 " --> pdb=" O ALA U 97 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP Q 452 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL U 166 " --> pdb=" O ASP Q 452 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU Q 454 " --> pdb=" O VAL U 166 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR W 164 " --> pdb=" O TYR Q 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 97 through 98 removed outlier: 3.757A pdb=" N ASP U 105 " --> pdb=" O ALA U 97 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP Q 452 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL U 166 " --> pdb=" O ASP Q 452 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU Q 454 " --> pdb=" O VAL U 166 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR W 164 " --> pdb=" O TYR Q 457 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 469 through 472 removed outlier: 3.687A pdb=" N GLN Q 469 " --> pdb=" O TYR Q 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 489 through 493 removed outlier: 3.968A pdb=" N GLY Q 489 " --> pdb=" O ILE Q 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 518 through 523 removed outlier: 6.154A pdb=" N LEU Q 518 " --> pdb=" O ASP Q 596 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 567 through 568 Processing sheet with id=AB1, first strand: chain 'Q' and resid 567 through 568 removed outlier: 5.727A pdb=" N LEU Q 537 " --> pdb=" O GLY Q 610 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY Q 610 " --> pdb=" O LEU Q 537 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER Q 539 " --> pdb=" O GLU Q 608 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN Q 604 " --> pdb=" O GLY Q 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 57 through 62 removed outlier: 3.507A pdb=" N GLY U 123 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N THR U 120 " --> pdb=" O SER U 147 " (cutoff:3.500A) removed outlier: 11.336A pdb=" N SER U 147 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR U 122 " --> pdb=" O PHE U 145 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER U 141 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 57 through 60 removed outlier: 6.760A pdb=" N GLY W 123 " --> pdb=" O SER W 147 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N SER W 147 " --> pdb=" O GLY W 123 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N PHE W 125 " --> pdb=" O PHE W 145 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N PHE W 145 " --> pdb=" O PHE W 125 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N VAL W 127 " --> pdb=" O VAL W 143 " (cutoff:3.500A) removed outlier: 12.572A pdb=" N VAL W 143 " --> pdb=" O VAL W 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 5 removed outlier: 8.749A pdb=" N MET B 122 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR B 114 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.522A pdb=" N ILE B 111 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 95 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 113 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 93 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 91 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 31 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 93 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG B 29 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET B 95 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 27 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 50 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 51 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 83 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP B 80 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.814A pdb=" N PHE C 92 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 28 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C 51 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 30 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 51 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR C 83 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 53 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP C 80 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 88 through 89 569 hydrogen bonds defined for protein. 1608 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: 1.31 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3695 1.34 - 1.46: 2378 1.46 - 1.58: 5009 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 11150 Sorted by residual: bond pdb=" CA SER Y 40 " pdb=" CB SER Y 40 " ideal model delta sigma weight residual 1.535 1.471 0.064 2.02e-02 2.45e+03 1.01e+01 bond pdb=" CA SER Y 37 " pdb=" CB SER Y 37 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.66e-02 3.63e+03 7.18e+00 bond pdb=" C ILE X 216 " pdb=" N PRO X 217 " ideal model delta sigma weight residual 1.334 1.354 -0.021 8.40e-03 1.42e+04 6.02e+00 bond pdb=" N SER Y 40 " pdb=" CA SER Y 40 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.47e+00 bond pdb=" N SER Y 37 " pdb=" CA SER Y 37 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.31e-02 5.83e+03 5.29e+00 ... (remaining 11145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 14926 2.03 - 4.06: 202 4.06 - 6.09: 32 6.09 - 8.11: 2 8.11 - 10.14: 1 Bond angle restraints: 15163 Sorted by residual: angle pdb=" N PRO Y 39 " pdb=" CA PRO Y 39 " pdb=" CB PRO Y 39 " ideal model delta sigma weight residual 103.35 99.00 4.35 8.70e-01 1.32e+00 2.50e+01 angle pdb=" C SER Y 37 " pdb=" N LYS Y 38 " pdb=" CA LYS Y 38 " ideal model delta sigma weight residual 123.16 118.47 4.69 1.23e+00 6.61e-01 1.46e+01 angle pdb=" CA PRO Y 39 " pdb=" C PRO Y 39 " pdb=" O PRO Y 39 " ideal model delta sigma weight residual 121.56 117.21 4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N PRO Y 39 " pdb=" CD PRO Y 39 " pdb=" CG PRO Y 39 " ideal model delta sigma weight residual 103.20 98.44 4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" CA SER Y 37 " pdb=" C SER Y 37 " pdb=" O SER Y 37 " ideal model delta sigma weight residual 121.81 118.08 3.73 1.18e+00 7.18e-01 1.00e+01 ... (remaining 15158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 5738 17.32 - 34.64: 743 34.64 - 51.95: 177 51.95 - 69.27: 23 69.27 - 86.59: 11 Dihedral angle restraints: 6692 sinusoidal: 2578 harmonic: 4114 Sorted by residual: dihedral pdb=" CA THR X 93 " pdb=" C THR X 93 " pdb=" N LYS X 94 " pdb=" CA LYS X 94 " ideal model delta harmonic sigma weight residual 180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ALA C 120 " pdb=" C ALA C 120 " pdb=" N ASP C 121 " pdb=" CA ASP C 121 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN W 79 " pdb=" C ASN W 79 " pdb=" N MET W 80 " pdb=" CA MET W 80 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1278 0.039 - 0.077: 349 0.077 - 0.116: 100 0.116 - 0.154: 16 0.154 - 0.193: 2 Chirality restraints: 1745 Sorted by residual: chirality pdb=" CA LYS Y 38 " pdb=" N LYS Y 38 " pdb=" C LYS Y 38 " pdb=" CB LYS Y 38 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA LYS X 94 " pdb=" N LYS X 94 " pdb=" C LYS X 94 " pdb=" CB LYS X 94 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA ILE W 163 " pdb=" N ILE W 163 " pdb=" C ILE W 163 " pdb=" CB ILE W 163 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1742 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 108 " -0.063 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO B 109 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 109 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 109 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 35 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C PRO Y 35 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO Y 35 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU Y 36 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 92 " 0.012 2.00e-02 2.50e+03 1.57e-02 4.29e+00 pdb=" CG PHE B 92 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 92 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 92 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 92 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 92 " -0.001 2.00e-02 2.50e+03 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2198 2.78 - 3.31: 9571 3.31 - 3.84: 16564 3.84 - 4.37: 17026 4.37 - 4.90: 32268 Nonbonded interactions: 77627 Sorted by model distance: nonbonded pdb=" O ARG B 20 " pdb=" OG1 THR B 24 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP W 75 " pdb=" ND2 ASN W 79 " model vdw 2.268 3.120 nonbonded pdb=" N GLU Q 511 " pdb=" OE1 GLU Q 511 " model vdw 2.281 3.120 nonbonded pdb=" NE1 TRP X 120 " pdb=" OE2 GLU Y 181 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR B 38 " pdb=" OD1 ASP B 40 " model vdw 2.289 3.040 ... (remaining 77622 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 2 through 55 or resid 59 through 101 or resid 105 through \ 145)) } ncs_group { reference = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'X' and resid 3 through 298) selection = chain 'Y' } 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: 31.220 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.064 11150 Z= 0.167 Angle : 0.585 10.142 15163 Z= 0.329 Chirality : 0.039 0.193 1745 Planarity : 0.004 0.095 1992 Dihedral : 16.285 86.588 4044 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 0.34 % Allowed : 21.80 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1409 helix: 3.59 (0.22), residues: 540 sheet: 0.51 (0.43), residues: 160 loop : -1.69 (0.20), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 29 TYR 0.013 0.001 TYR X 241 PHE 0.036 0.001 PHE B 92 TRP 0.015 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (11150) covalent geometry : angle 0.58517 / 0.33 (15163) hydrogen bonds : bond 0.16462 / 11.04 ( 553) hydrogen bonds : angle 5.63153 / 3.75 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.290 Fit side-chains REVERT: Y 137 GLN cc_start: 0.7558 (tp40) cc_final: 0.7214 (tp-100) outliers start: 4 outliers final: 4 residues processed: 179 average time/residue: 0.1139 time to fit residues: 28.2216 Evaluate side-chains 170 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 350 THR Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain W residue 155 GLN Chi-restraints excluded: chain B residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 85 ASN Y 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104362 restraints weight = 16969.933| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.95 r_work: 0.3105 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11150 Z= 0.134 Angle : 0.520 6.266 15163 Z= 0.272 Chirality : 0.039 0.165 1745 Planarity : 0.004 0.068 1992 Dihedral : 4.033 46.110 1558 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 2.21 % Allowed : 21.46 % Favored : 76.34 % 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: 1.28 (0.23), residues: 1409 helix: 3.67 (0.22), residues: 542 sheet: 0.65 (0.43), residues: 164 loop : -1.54 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 164 TYR 0.012 0.001 TYR Q 541 PHE 0.011 0.001 PHE W 61 TRP 0.010 0.001 TRP X 120 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (11150) covalent geometry : angle 0.51988 / 0.27 (15163) hydrogen bonds : bond 0.07472 / 5.03 ( 553) hydrogen bonds : angle 4.22460 / 2.85 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.422 Fit side-chains REVERT: Q 495 ASN cc_start: 0.8459 (m-40) cc_final: 0.8011 (t0) REVERT: Y 12 ASP cc_start: 0.8231 (t0) cc_final: 0.7884 (t0) REVERT: Y 16 ASP cc_start: 0.7635 (m-30) cc_final: 0.7358 (m-30) REVERT: Y 137 GLN cc_start: 0.8477 (tp40) cc_final: 0.8230 (tp40) REVERT: B 95 MET cc_start: 0.8850 (ttm) cc_final: 0.8612 (ttm) outliers start: 26 outliers final: 16 residues processed: 189 average time/residue: 0.1010 time to fit residues: 27.0268 Evaluate side-chains 177 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 539 SER Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 278 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 21 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [134, 5, 83, 127, 63, 92, 137, 84, 15, 8, 56] chunk 134 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102597 restraints weight = 17209.490| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.95 r_work: 0.3077 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11150 Z= 0.156 Angle : 0.522 6.276 15163 Z= 0.272 Chirality : 0.040 0.167 1745 Planarity : 0.004 0.059 1992 Dihedral : 3.751 27.547 1552 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.90 % Favored : 96.03 % Rotamer: Outliers : 2.12 % Allowed : 22.22 % Favored : 75.66 % 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: 1.23 (0.23), residues: 1409 helix: 3.61 (0.22), residues: 542 sheet: 0.71 (0.41), residues: 170 loop : -1.60 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 164 TYR 0.012 0.001 TYR Y 210 PHE 0.012 0.001 PHE U 61 TRP 0.009 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (11150) covalent geometry : angle 0.52197 / 0.27 (15163) hydrogen bonds : bond 0.07804 / 5.23 ( 553) hydrogen bonds : angle 4.07668 / 2.75 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.364 Fit side-chains REVERT: Q 459 ASN cc_start: 0.8994 (m-40) cc_final: 0.8684 (m-40) REVERT: W 45 SER cc_start: 0.9365 (t) cc_final: 0.8906 (m) REVERT: Y 12 ASP cc_start: 0.8315 (t0) cc_final: 0.7957 (t0) REVERT: Y 16 ASP cc_start: 0.7759 (m-30) cc_final: 0.7465 (m-30) REVERT: Y 75 GLU cc_start: 0.5774 (tt0) cc_final: 0.5252 (tt0) REVERT: Y 292 ASP cc_start: 0.8593 (t0) cc_final: 0.8228 (m-30) REVERT: C 5 TYR cc_start: 0.8812 (m-10) cc_final: 0.8594 (m-10) outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 0.1046 time to fit residues: 26.4378 Evaluate side-chains 178 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 90 CYS Chi-restraints excluded: chain Y residue 278 ASN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 101 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [11, 101, 95, 12, 100, 64, 49, 37, 59, 69, 131] chunk 11 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098177 restraints weight = 17260.957| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.95 r_work: 0.3026 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11150 Z= 0.211 Angle : 0.575 7.313 15163 Z= 0.300 Chirality : 0.042 0.187 1745 Planarity : 0.004 0.057 1992 Dihedral : 3.946 27.499 1552 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 3.82 % Allowed : 21.71 % Favored : 74.47 % 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: 1.03 (0.23), residues: 1409 helix: 3.39 (0.22), residues: 542 sheet: 0.76 (0.42), residues: 160 loop : -1.67 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 164 TYR 0.016 0.001 TYR Y 210 PHE 0.019 0.002 PHE B 92 TRP 0.011 0.001 TRP X 98 HIS 0.002 0.001 HIS Y 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (11150) covalent geometry : angle 0.57478 / 0.30 (15163) hydrogen bonds : bond 0.08817 / 5.87 ( 553) hydrogen bonds : angle 4.18449 / 2.83 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.372 Fit side-chains REVERT: Q 459 ASN cc_start: 0.8936 (m-40) cc_final: 0.8577 (m-40) REVERT: Q 537 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9003 (mp) REVERT: U 34 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8378 (mm) REVERT: W 45 SER cc_start: 0.9383 (t) cc_final: 0.8904 (m) REVERT: X 81 GLU cc_start: 0.8848 (tp30) cc_final: 0.8381 (tp30) REVERT: Y 12 ASP cc_start: 0.8351 (t0) cc_final: 0.8023 (t0) REVERT: Y 16 ASP cc_start: 0.7813 (m-30) cc_final: 0.7525 (m-30) REVERT: Y 75 GLU cc_start: 0.5770 (tt0) cc_final: 0.4788 (tt0) REVERT: Y 137 GLN cc_start: 0.8563 (tp40) cc_final: 0.8269 (tp40) REVERT: Y 279 SER cc_start: 0.9100 (t) cc_final: 0.8643 (p) REVERT: Y 292 ASP cc_start: 0.8529 (t0) cc_final: 0.8131 (m-30) outliers start: 45 outliers final: 31 residues processed: 199 average time/residue: 0.1060 time to fit residues: 29.9233 Evaluate side-chains 200 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 407 LEU Chi-restraints excluded: chain Q residue 537 LEU Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 188 MET Chi-restraints excluded: chain X residue 301 GLN Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 90 CYS Chi-restraints excluded: chain Y residue 133 SER Chi-restraints excluded: chain Y residue 277 ASN Chi-restraints excluded: chain Y residue 278 ASN Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 123 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [111, 118, 126, 50, 28, 51, 83, 93, 44, 129, 89] chunk 111 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103332 restraints weight = 17134.936| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.95 r_work: 0.3093 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11150 Z= 0.130 Angle : 0.502 6.724 15163 Z= 0.261 Chirality : 0.039 0.183 1745 Planarity : 0.003 0.052 1992 Dihedral : 3.719 25.618 1552 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 2.46 % Allowed : 23.49 % Favored : 74.05 % 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: 1.26 (0.23), residues: 1409 helix: 3.64 (0.22), residues: 542 sheet: 0.83 (0.42), residues: 170 loop : -1.62 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 164 TYR 0.011 0.001 TYR U 86 PHE 0.011 0.001 PHE X 190 TRP 0.011 0.001 TRP X 98 HIS 0.003 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (11150) covalent geometry : angle 0.50233 / 0.26 (15163) hydrogen bonds : bond 0.07408 / 4.97 ( 553) hydrogen bonds : angle 3.93179 / 2.65 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.272 Fit side-chains REVERT: Q 459 ASN cc_start: 0.8909 (m-40) cc_final: 0.8565 (m-40) REVERT: Q 495 ASN cc_start: 0.8603 (m-40) cc_final: 0.8237 (t0) REVERT: W 45 SER cc_start: 0.9304 (t) cc_final: 0.8863 (m) REVERT: Y 12 ASP cc_start: 0.8289 (t0) cc_final: 0.7959 (t0) REVERT: Y 16 ASP cc_start: 0.7762 (m-30) cc_final: 0.7443 (m-30) REVERT: Y 75 GLU cc_start: 0.5662 (tt0) cc_final: 0.4644 (tt0) REVERT: Y 163 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: Y 292 ASP cc_start: 0.8491 (t0) cc_final: 0.8270 (t0) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.1108 time to fit residues: 29.5276 Evaluate side-chains 182 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 521 LEU Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain W residue 115 VAL Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [60, 23, 21, 35, 27, 128, 20, 2, 46, 16, 116] chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096964 restraints weight = 17414.202| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.96 r_work: 0.2998 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11150 Z= 0.255 Angle : 0.618 9.857 15163 Z= 0.321 Chirality : 0.043 0.176 1745 Planarity : 0.004 0.065 1992 Dihedral : 4.045 25.604 1552 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 3.65 % Allowed : 22.90 % Favored : 73.45 % 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: 0.92 (0.23), residues: 1409 helix: 3.26 (0.22), residues: 544 sheet: 0.85 (0.44), residues: 150 loop : -1.73 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 164 TYR 0.017 0.002 TYR Y 210 PHE 0.020 0.002 PHE W 56 TRP 0.011 0.002 TRP Y 79 HIS 0.003 0.001 HIS Y 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.25 (11150) covalent geometry : angle 0.61821 / 0.32 (15163) hydrogen bonds : bond 0.09339 / 6.21 ( 553) hydrogen bonds : angle 4.23006 / 2.86 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.397 Fit side-chains REVERT: U 158 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8777 (mm110) REVERT: X 245 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: Y 12 ASP cc_start: 0.8389 (t0) cc_final: 0.8073 (t0) REVERT: Y 16 ASP cc_start: 0.7795 (m-30) cc_final: 0.7518 (m-30) REVERT: Y 75 GLU cc_start: 0.5797 (tt0) cc_final: 0.4101 (tt0) REVERT: Y 279 SER cc_start: 0.9104 (t) cc_final: 0.8671 (p) REVERT: Y 292 ASP cc_start: 0.8542 (t0) cc_final: 0.8230 (m-30) outliers start: 43 outliers final: 31 residues processed: 189 average time/residue: 0.1028 time to fit residues: 27.2860 Evaluate side-chains 191 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 158 GLN Chi-restraints excluded: chain W residue 143 VAL Chi-restraints excluded: chain W residue 156 THR Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 232 SER Chi-restraints excluded: chain X residue 245 GLU Chi-restraints excluded: chain X residue 301 GLN Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 90 CYS Chi-restraints excluded: chain Y residue 133 SER Chi-restraints excluded: chain Y residue 277 ASN Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 123 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [15, 4, 123, 138, 91, 9, 46, 87, 1, 136, 33] chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103283 restraints weight = 17040.473| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.95 r_work: 0.3092 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11150 Z= 0.130 Angle : 0.510 8.090 15163 Z= 0.265 Chirality : 0.039 0.162 1745 Planarity : 0.003 0.051 1992 Dihedral : 3.728 24.435 1552 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.87 % Allowed : 24.68 % Favored : 73.45 % 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: 1.29 (0.23), residues: 1409 helix: 3.70 (0.22), residues: 541 sheet: 0.85 (0.42), residues: 170 loop : -1.63 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 145 TYR 0.014 0.001 TYR X 43 PHE 0.011 0.001 PHE X 190 TRP 0.011 0.001 TRP X 98 HIS 0.003 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11150) covalent geometry : angle 0.51015 / 0.27 (15163) hydrogen bonds : bond 0.07377 / 4.94 ( 553) hydrogen bonds : angle 3.91624 / 2.64 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.492 Fit side-chains REVERT: W 45 SER cc_start: 0.9280 (t) cc_final: 0.8849 (m) REVERT: X 81 GLU cc_start: 0.8835 (tp30) cc_final: 0.8438 (tp30) REVERT: Y 12 ASP cc_start: 0.8276 (t0) cc_final: 0.7962 (t0) REVERT: Y 16 ASP cc_start: 0.7699 (m-30) cc_final: 0.7403 (m-30) REVERT: Y 75 GLU cc_start: 0.5403 (tt0) cc_final: 0.4132 (tt0) REVERT: Y 163 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: Y 279 SER cc_start: 0.9045 (t) cc_final: 0.8642 (p) REVERT: C 112 GLN cc_start: 0.8929 (tt0) cc_final: 0.8702 (tt0) outliers start: 22 outliers final: 19 residues processed: 182 average time/residue: 0.0978 time to fit residues: 25.2167 Evaluate side-chains 184 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [28, 26, 93, 131, 23, 82, 9, 21, 94, 90, 5] chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100951 restraints weight = 17151.054| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.94 r_work: 0.3049 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11150 Z= 0.164 Angle : 0.534 8.013 15163 Z= 0.276 Chirality : 0.041 0.197 1745 Planarity : 0.004 0.050 1992 Dihedral : 3.696 24.280 1550 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 2.29 % Allowed : 24.68 % Favored : 73.03 % 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: 1.19 (0.23), residues: 1409 helix: 3.63 (0.22), residues: 541 sheet: 0.84 (0.43), residues: 156 loop : -1.66 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 164 TYR 0.012 0.001 TYR Y 210 PHE 0.014 0.001 PHE U 61 TRP 0.009 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (11150) covalent geometry : angle 0.53436 / 0.28 (15163) hydrogen bonds : bond 0.07912 / 5.29 ( 553) hydrogen bonds : angle 3.94961 / 2.67 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.420 Fit side-chains REVERT: W 45 SER cc_start: 0.9297 (t) cc_final: 0.8844 (m) REVERT: X 81 GLU cc_start: 0.8849 (tp30) cc_final: 0.8462 (tp30) REVERT: Y 12 ASP cc_start: 0.8295 (t0) cc_final: 0.7975 (t0) REVERT: Y 16 ASP cc_start: 0.7717 (m-30) cc_final: 0.7423 (m-30) REVERT: Y 75 GLU cc_start: 0.5565 (tt0) cc_final: 0.3728 (tt0) REVERT: Y 163 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: Y 279 SER cc_start: 0.9093 (t) cc_final: 0.8680 (p) REVERT: B 31 TYR cc_start: 0.7799 (m-80) cc_final: 0.7361 (m-80) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.1046 time to fit residues: 26.3548 Evaluate side-chains 185 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 521 LEU Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 229 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [53, 102, 40, 3, 35, 55, 108, 25, 34, 127, 63] chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 63 optimal weight: 0.0370 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099323 restraints weight = 17062.574| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.94 r_work: 0.3041 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11150 Z= 0.187 Angle : 0.563 9.151 15163 Z= 0.292 Chirality : 0.041 0.188 1745 Planarity : 0.004 0.049 1992 Dihedral : 3.789 24.705 1550 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 2.71 % Allowed : 24.00 % Favored : 73.28 % 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: 1.11 (0.23), residues: 1409 helix: 3.52 (0.22), residues: 541 sheet: 0.96 (0.44), residues: 150 loop : -1.69 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 164 TYR 0.013 0.001 TYR Y 210 PHE 0.016 0.002 PHE U 61 TRP 0.009 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11150) covalent geometry : angle 0.56315 / 0.29 (15163) hydrogen bonds : bond 0.08354 / 5.57 ( 553) hydrogen bonds : angle 4.01641 / 2.72 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.325 Fit side-chains REVERT: W 45 SER cc_start: 0.9331 (t) cc_final: 0.8896 (m) REVERT: X 41 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8775 (mp) REVERT: X 81 GLU cc_start: 0.8855 (tp30) cc_final: 0.8501 (tp30) REVERT: Y 12 ASP cc_start: 0.8331 (t0) cc_final: 0.8005 (t0) REVERT: Y 16 ASP cc_start: 0.7745 (m-30) cc_final: 0.7449 (m-30) REVERT: Y 75 GLU cc_start: 0.5595 (tt0) cc_final: 0.3729 (tt0) REVERT: Y 163 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: Y 279 SER cc_start: 0.9101 (t) cc_final: 0.8687 (p) REVERT: B 31 TYR cc_start: 0.7823 (m-80) cc_final: 0.7454 (m-80) outliers start: 32 outliers final: 28 residues processed: 180 average time/residue: 0.1091 time to fit residues: 27.7360 Evaluate side-chains 189 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 143 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 229 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [102, 134, 71, 5, 95, 23, 103, 76, 82, 63, 69] chunk 102 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 69 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099748 restraints weight = 17114.520| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.95 r_work: 0.3033 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11150 Z= 0.174 Angle : 0.551 9.632 15163 Z= 0.285 Chirality : 0.041 0.184 1745 Planarity : 0.004 0.049 1992 Dihedral : 3.768 24.783 1550 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Rotamer: Outliers : 2.71 % Allowed : 24.34 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.23), residues: 1409 helix: 3.51 (0.22), residues: 541 sheet: 0.96 (0.44), residues: 150 loop : -1.69 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 164 TYR 0.016 0.001 TYR C 5 PHE 0.015 0.001 PHE U 61 TRP 0.010 0.001 TRP X 98 HIS 0.002 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (11150) covalent geometry : angle 0.55118 / 0.29 (15163) hydrogen bonds : bond 0.08228 / 5.49 ( 553) hydrogen bonds : angle 4.01045 / 2.71 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.408 Fit side-chains REVERT: U 34 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8372 (mm) REVERT: W 45 SER cc_start: 0.9318 (t) cc_final: 0.8888 (m) REVERT: X 41 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8785 (mp) REVERT: X 81 GLU cc_start: 0.8869 (tp30) cc_final: 0.8525 (tp30) REVERT: Y 12 ASP cc_start: 0.8312 (t0) cc_final: 0.8009 (t0) REVERT: Y 16 ASP cc_start: 0.7730 (m-30) cc_final: 0.7455 (m-30) REVERT: Y 75 GLU cc_start: 0.5534 (tt0) cc_final: 0.3670 (tt0) REVERT: Y 163 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: Y 279 SER cc_start: 0.9098 (t) cc_final: 0.8683 (p) REVERT: B 31 TYR cc_start: 0.7740 (m-80) cc_final: 0.7399 (m-80) REVERT: C 5 TYR cc_start: 0.8885 (m-10) cc_final: 0.8625 (m-10) outliers start: 32 outliers final: 26 residues processed: 184 average time/residue: 0.1057 time to fit residues: 27.4997 Evaluate side-chains 192 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 396 VAL Chi-restraints excluded: chain Q residue 406 VAL Chi-restraints excluded: chain Q residue 452 ASP Chi-restraints excluded: chain Q residue 552 PHE Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 101 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 41 LEU Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 163 GLU Chi-restraints excluded: chain Y residue 229 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: [16, 98, 0, 31, 121, 60, 77, 104, 101, 94, 93] chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104842 restraints weight = 17075.701| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.95 r_work: 0.3122 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11150 Z= 0.123 Angle : 0.509 10.396 15163 Z= 0.261 Chirality : 0.039 0.182 1745 Planarity : 0.003 0.048 1992 Dihedral : 3.544 23.666 1550 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 2.37 % Allowed : 24.43 % Favored : 73.20 % 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: 1.38 (0.23), residues: 1409 helix: 3.81 (0.22), residues: 540 sheet: 1.03 (0.43), residues: 161 loop : -1.60 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 94 TYR 0.013 0.001 TYR C 5 PHE 0.012 0.001 PHE X 190 TRP 0.014 0.001 TRP X 98 HIS 0.001 0.001 HIS X 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11150) covalent geometry : angle 0.50920 / 0.26 (15163) hydrogen bonds : bond 0.06825 / 4.59 ( 553) hydrogen bonds : angle 3.77573 / 2.54 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3847.45 seconds wall clock time: 66 minutes 18.20 seconds (3978.20 seconds total)