Starting phenix.real_space_refine on Thu Mar 5 14:29:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adg_15362/03_2026/8adg_15362.map" } resolution = 3.0 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= 0.051 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 S 32 5.16 5 C 7440 2.51 5 N 2019 2.21 5 O 2317 1.98 5 H 11383 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12167 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5393 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 11, 'TRANS': 349} Chain breaks: 1 Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 845 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3348 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1292 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.15 Number of scatterers: 23191 At special positions: 0 Unit cell: (97.75, 133.45, 125.8, 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 32 16.00 O 2317 8.00 N 2019 7.00 C 7440 6.00 H 11383 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 767.5 milliseconds 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 24.2% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.019A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.795A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.042A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 497 through 500 removed outlier: 3.980A pdb=" N ASP A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.607A pdb=" N TYR A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.616A pdb=" N GLY A 695 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'C' and resid 31 through 39 removed outlier: 4.039A pdb=" N VAL C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.080A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.502A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.669A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.659A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.529A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.815A pdb=" N ILE E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.357A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.428A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.460A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N SER B 193 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 245 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.251A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.623A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA A 343 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN A 276 " --> pdb=" O ALA A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.251A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.623A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.715A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.519A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50 removed outlier: 5.157A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.610A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 117 removed outlier: 6.245A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.765A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202 removed outlier: 6.733A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.517A pdb=" N ALA B 269 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.543A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.807A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.036A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 525 hydrogen bonds defined for protein. 1467 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: 6.24 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11339 1.03 - 1.23: 59 1.23 - 1.42: 5210 1.42 - 1.61: 6781 1.61 - 1.81: 62 Bond restraints: 23451 Sorted by residual: bond pdb=" CG PRO B 34 " pdb=" CD PRO B 34 " ideal model delta sigma weight residual 1.503 1.047 0.456 3.40e-02 8.65e+02 1.80e+02 bond pdb=" C UX8 F 3 " pdb=" O UX8 F 3 " ideal model delta sigma weight residual 1.231 1.395 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" CZ2 TRP F 1 " pdb=" HZ2 TRP F 1 " ideal model delta sigma weight residual 0.930 1.090 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CZ3 UX8 F 3 " pdb=" HZ3 UX8 F 3 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TRP F 7 " pdb=" HD1 TRP F 7 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 23446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 42151 4.92 - 9.83: 11 9.83 - 14.75: 5 14.75 - 19.67: 3 19.67 - 24.59: 1 Bond angle restraints: 42171 Sorted by residual: angle pdb=" N PRO B 34 " pdb=" CD PRO B 34 " pdb=" CG PRO B 34 " ideal model delta sigma weight residual 103.20 78.61 24.59 1.50e+00 4.44e-01 2.69e+02 angle pdb=" CA PRO B 34 " pdb=" CB PRO B 34 " pdb=" CG PRO B 34 " ideal model delta sigma weight residual 104.50 87.73 16.77 1.90e+00 2.77e-01 7.79e+01 angle pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" CD PRO B 34 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.49e+01 angle pdb=" CA LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB2 LYS F 5 " ideal model delta sigma weight residual 109.00 90.49 18.51 3.00e+00 1.11e-01 3.81e+01 angle pdb=" CG LYS F 5 " pdb=" CB LYS F 5 " pdb=" HB2 LYS F 5 " ideal model delta sigma weight residual 108.00 90.51 17.49 3.00e+00 1.11e-01 3.40e+01 ... (remaining 42166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10129 17.96 - 35.91: 726 35.91 - 53.87: 198 53.87 - 71.82: 46 71.82 - 89.78: 14 Dihedral angle restraints: 11113 sinusoidal: 5987 harmonic: 5126 Sorted by residual: dihedral pdb=" CD2 TRP F 1 " pdb=" CE2 TRP F 1 " pdb=" CZ2 TRP F 1 " pdb=" HZ2 TRP F 1 " ideal model delta harmonic sigma weight residual -180.00 -125.33 -54.67 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -131.25 45.25 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA LEU A 699 " pdb=" C LEU A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 994 0.029 - 0.058: 521 0.058 - 0.087: 115 0.087 - 0.116: 109 0.116 - 0.145: 44 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE B 296 " pdb=" N ILE B 296 " pdb=" C ILE B 296 " pdb=" CB ILE B 296 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE E 104 " pdb=" N ILE E 104 " pdb=" C ILE E 104 " pdb=" CB ILE E 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1780 not shown) Planarity restraints: 3593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 1 " -0.129 2.00e-02 2.50e+03 1.84e-01 1.27e+03 pdb=" CG TRP F 1 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 1 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP F 1 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP F 1 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP F 1 " 0.108 2.00e-02 2.50e+03 pdb=" CE3 TRP F 1 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 1 " 0.183 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 1 " 0.068 2.00e-02 2.50e+03 pdb=" CH2 TRP F 1 " 0.159 2.00e-02 2.50e+03 pdb=" HD1 TRP F 1 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP F 1 " 0.155 2.00e-02 2.50e+03 pdb=" HE3 TRP F 1 " -0.078 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 1 " -0.608 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 1 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 546 " -0.034 2.00e-02 2.50e+03 2.19e-02 1.92e+01 pdb=" CG TRP A 546 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 546 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 546 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 546 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 546 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 546 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 546 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 546 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 TRP A 546 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 546 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 546 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 546 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 546 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 546 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 33 " -0.042 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 34 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " -0.031 5.00e-02 4.00e+02 ... (remaining 3590 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 591 2.15 - 2.76: 42757 2.76 - 3.37: 61231 3.37 - 3.99: 81598 3.99 - 4.60: 128113 Nonbonded interactions: 314290 Sorted by model distance: nonbonded pdb=" OD1 ASP C 38 " pdb=" H GLU C 39 " model vdw 1.533 2.450 nonbonded pdb=" OD1 ASN E 96 " pdb=" H SER E 98 " model vdw 1.584 2.450 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.614 2.450 nonbonded pdb=" O ARG A 661 " pdb=" HG SER A 769 " model vdw 1.614 2.450 nonbonded pdb="HE21 GLN B 319 " pdb=" O GLY B 354 " model vdw 1.620 2.450 ... (remaining 314285 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.456 12071 Z= 0.232 Angle : 0.622 24.587 16405 Z= 0.351 Chirality : 0.044 0.145 1783 Planarity : 0.004 0.058 2158 Dihedral : 14.028 89.781 4366 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.24 (0.21), residues: 1487 helix: 2.32 (0.29), residues: 326 sheet: 0.30 (0.25), residues: 445 loop : -0.98 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 583 TYR 0.015 0.001 TYR A 794 PHE 0.015 0.001 PHE A 791 TRP 0.072 0.002 TRP A 546 HIS 0.014 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00603 (12068) covalent geometry : angle 0.62218 (16403) SS BOND : bond 0.00403 ( 1) SS BOND : angle 1.81828 ( 2) hydrogen bonds : bond 0.08422 ( 521) hydrogen bonds : angle 4.92835 ( 1467) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 ASN cc_start: 0.7563 (t0) cc_final: 0.7287 (t0) REVERT: B 268 THR cc_start: 0.8547 (t) cc_final: 0.8294 (m) REVERT: C 41 TYR cc_start: 0.6295 (p90) cc_final: 0.6046 (p90) REVERT: D 93 ASP cc_start: 0.8091 (m-30) cc_final: 0.7728 (m-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.0515 time to fit residues: 155.1161 Evaluate side-chains 110 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 561 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127915 restraints weight = 35449.787| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12071 Z= 0.171 Angle : 0.533 7.358 16405 Z= 0.284 Chirality : 0.044 0.147 1783 Planarity : 0.004 0.042 2158 Dihedral : 4.261 20.135 1651 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.35 % Allowed : 5.70 % Favored : 92.95 % 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: 0.24 (0.21), residues: 1487 helix: 2.28 (0.28), residues: 326 sheet: 0.37 (0.25), residues: 439 loop : -0.99 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 583 TYR 0.010 0.001 TYR D 79 PHE 0.015 0.001 PHE A 426 TRP 0.021 0.002 TRP A 546 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00413 (12068) covalent geometry : angle 0.53296 (16403) SS BOND : bond 0.00396 ( 1) SS BOND : angle 1.64387 ( 2) hydrogen bonds : bond 0.04830 ( 521) hydrogen bonds : angle 4.66168 ( 1467) Misc. bond : bond 0.00458 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6718 (mm-30) REVERT: A 286 GLN cc_start: 0.7464 (mp10) cc_final: 0.6536 (tm130) REVERT: A 520 ASN cc_start: 0.8064 (t0) cc_final: 0.7617 (t0) REVERT: B 70 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 268 THR cc_start: 0.8541 (t) cc_final: 0.8277 (m) REVERT: C 41 TYR cc_start: 0.6801 (p90) cc_final: 0.6178 (p90) REVERT: C 76 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7608 (p) REVERT: D 93 ASP cc_start: 0.8231 (m-30) cc_final: 0.7757 (m-30) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 1.0588 time to fit residues: 140.6243 Evaluate side-chains 119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 GLN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.170918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124501 restraints weight = 35266.174| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.16 r_work: 0.3209 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12071 Z= 0.160 Angle : 0.515 7.441 16405 Z= 0.274 Chirality : 0.043 0.146 1783 Planarity : 0.004 0.044 2158 Dihedral : 4.238 18.885 1651 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.27 % Allowed : 7.13 % Favored : 91.61 % 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: 0.17 (0.21), residues: 1487 helix: 2.30 (0.28), residues: 326 sheet: 0.17 (0.24), residues: 449 loop : -0.97 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 583 TYR 0.013 0.001 TYR D 79 PHE 0.015 0.001 PHE A 426 TRP 0.011 0.001 TRP B 348 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00385 (12068) covalent geometry : angle 0.51474 (16403) SS BOND : bond 0.00329 ( 1) SS BOND : angle 1.65619 ( 2) hydrogen bonds : bond 0.04546 ( 521) hydrogen bonds : angle 4.55216 ( 1467) Misc. bond : bond 0.00463 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8331 (p0) cc_final: 0.8119 (p0) REVERT: A 286 GLN cc_start: 0.7403 (mp10) cc_final: 0.6434 (tm130) REVERT: A 520 ASN cc_start: 0.8004 (t0) cc_final: 0.7409 (t0) REVERT: A 521 GLU cc_start: 0.7314 (tt0) cc_final: 0.7002 (pt0) REVERT: A 614 ASP cc_start: 0.8376 (m-30) cc_final: 0.8089 (m-30) REVERT: B 70 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (t0) REVERT: B 266 ASN cc_start: 0.6959 (p0) cc_final: 0.6577 (p0) REVERT: B 268 THR cc_start: 0.8522 (t) cc_final: 0.8188 (m) REVERT: C 41 TYR cc_start: 0.6811 (p90) cc_final: 0.6220 (p90) REVERT: D 93 ASP cc_start: 0.8224 (m-30) cc_final: 0.7743 (m-30) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 1.0547 time to fit residues: 142.7847 Evaluate side-chains 120 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 319 GLN B 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125168 restraints weight = 35409.706| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.07 r_work: 0.3200 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12071 Z= 0.184 Angle : 0.531 7.951 16405 Z= 0.283 Chirality : 0.044 0.154 1783 Planarity : 0.004 0.045 2158 Dihedral : 4.306 18.592 1651 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.43 % Allowed : 8.47 % Favored : 90.10 % 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: 0.04 (0.21), residues: 1487 helix: 2.11 (0.28), residues: 330 sheet: 0.13 (0.25), residues: 447 loop : -1.05 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 583 TYR 0.011 0.001 TYR D 79 PHE 0.015 0.001 PHE A 426 TRP 0.011 0.002 TRP B 143 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00448 (12068) covalent geometry : angle 0.53078 (16403) SS BOND : bond 0.00391 ( 1) SS BOND : angle 1.57166 ( 2) hydrogen bonds : bond 0.04704 ( 521) hydrogen bonds : angle 4.56479 ( 1467) Misc. bond : bond 0.00433 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8372 (p0) cc_final: 0.8155 (p0) REVERT: A 286 GLN cc_start: 0.7388 (mp10) cc_final: 0.6433 (tm130) REVERT: A 520 ASN cc_start: 0.8073 (t0) cc_final: 0.7538 (t0) REVERT: A 521 GLU cc_start: 0.7429 (tt0) cc_final: 0.7105 (pt0) REVERT: A 614 ASP cc_start: 0.8357 (m-30) cc_final: 0.8100 (m-30) REVERT: B 70 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8145 (t0) REVERT: B 268 THR cc_start: 0.8526 (t) cc_final: 0.8251 (m) REVERT: C 41 TYR cc_start: 0.6835 (p90) cc_final: 0.6235 (p90) REVERT: D 93 ASP cc_start: 0.8127 (m-30) cc_final: 0.7661 (m-30) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 1.0926 time to fit residues: 146.9731 Evaluate side-chains 122 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 359 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 146 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 266 ASN B 319 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124638 restraints weight = 35122.148| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.11 r_work: 0.3220 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12071 Z= 0.122 Angle : 0.491 7.174 16405 Z= 0.262 Chirality : 0.043 0.157 1783 Planarity : 0.004 0.045 2158 Dihedral : 4.193 17.514 1651 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.58 % Allowed : 8.87 % Favored : 89.55 % 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: 0.22 (0.22), residues: 1487 helix: 2.44 (0.28), residues: 326 sheet: 0.20 (0.25), residues: 443 loop : -0.98 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 583 TYR 0.010 0.001 TYR D 79 PHE 0.015 0.001 PHE A 426 TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00284 (12068) covalent geometry : angle 0.49064 (16403) SS BOND : bond 0.00320 ( 1) SS BOND : angle 1.42626 ( 2) hydrogen bonds : bond 0.04125 ( 521) hydrogen bonds : angle 4.46372 ( 1467) Misc. bond : bond 0.00400 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8307 (p0) cc_final: 0.8082 (p0) REVERT: A 286 GLN cc_start: 0.7296 (mp10) cc_final: 0.6323 (tm130) REVERT: A 520 ASN cc_start: 0.7957 (t0) cc_final: 0.7365 (t0) REVERT: A 521 GLU cc_start: 0.7324 (tt0) cc_final: 0.7020 (pt0) REVERT: A 614 ASP cc_start: 0.8352 (m-30) cc_final: 0.8035 (m-30) REVERT: B 70 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8126 (t0) REVERT: B 245 SER cc_start: 0.6321 (OUTLIER) cc_final: 0.6097 (m) REVERT: B 268 THR cc_start: 0.8435 (t) cc_final: 0.8179 (m) REVERT: C 41 TYR cc_start: 0.6662 (p90) cc_final: 0.6069 (p90) REVERT: C 76 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7539 (p) REVERT: D 93 ASP cc_start: 0.8206 (m-30) cc_final: 0.7735 (m-30) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 1.0831 time to fit residues: 146.1570 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 135 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 266 ASN B 359 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125150 restraints weight = 35476.288| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.09 r_work: 0.3200 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12071 Z= 0.188 Angle : 0.534 8.256 16405 Z= 0.284 Chirality : 0.044 0.146 1783 Planarity : 0.004 0.053 2158 Dihedral : 4.311 18.070 1651 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.50 % Allowed : 10.29 % Favored : 88.20 % 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: 0.05 (0.21), residues: 1487 helix: 2.17 (0.28), residues: 330 sheet: 0.15 (0.25), residues: 441 loop : -1.09 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 583 TYR 0.011 0.001 TYR D 79 PHE 0.016 0.001 PHE A 426 TRP 0.011 0.002 TRP B 143 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00457 (12068) covalent geometry : angle 0.53389 (16403) SS BOND : bond 0.00387 ( 1) SS BOND : angle 1.43285 ( 2) hydrogen bonds : bond 0.04689 ( 521) hydrogen bonds : angle 4.53211 ( 1467) Misc. bond : bond 0.00401 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8413 (p0) cc_final: 0.8176 (p0) REVERT: A 286 GLN cc_start: 0.7318 (mp10) cc_final: 0.6381 (tm130) REVERT: A 520 ASN cc_start: 0.8094 (t0) cc_final: 0.7669 (t0) REVERT: A 614 ASP cc_start: 0.8328 (m-30) cc_final: 0.8071 (m-30) REVERT: B 70 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 268 THR cc_start: 0.8478 (t) cc_final: 0.8219 (m) REVERT: C 41 TYR cc_start: 0.6699 (p90) cc_final: 0.6170 (p90) REVERT: C 76 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7727 (p) REVERT: D 93 ASP cc_start: 0.8136 (m-30) cc_final: 0.7683 (m-30) outliers start: 19 outliers final: 14 residues processed: 120 average time/residue: 1.0850 time to fit residues: 142.7827 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 42 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 143 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN D 44 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124694 restraints weight = 35347.068| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.11 r_work: 0.3223 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12071 Z= 0.123 Angle : 0.488 7.331 16405 Z= 0.260 Chirality : 0.043 0.141 1783 Planarity : 0.004 0.054 2158 Dihedral : 4.175 17.035 1651 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.58 % Allowed : 10.37 % Favored : 88.04 % 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: 0.21 (0.22), residues: 1487 helix: 2.37 (0.29), residues: 330 sheet: 0.22 (0.25), residues: 443 loop : -1.00 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 583 TYR 0.009 0.001 TYR D 79 PHE 0.016 0.001 PHE A 426 TRP 0.011 0.001 TRP B 348 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00290 (12068) covalent geometry : angle 0.48806 (16403) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.34442 ( 2) hydrogen bonds : bond 0.04079 ( 521) hydrogen bonds : angle 4.41731 ( 1467) Misc. bond : bond 0.00384 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8355 (p0) cc_final: 0.8148 (p0) REVERT: A 286 GLN cc_start: 0.7295 (mp10) cc_final: 0.6353 (tm130) REVERT: A 520 ASN cc_start: 0.8028 (t0) cc_final: 0.7473 (t0) REVERT: A 521 GLU cc_start: 0.7275 (tt0) cc_final: 0.7059 (pt0) REVERT: A 614 ASP cc_start: 0.8337 (m-30) cc_final: 0.8028 (m-30) REVERT: B 268 THR cc_start: 0.8455 (t) cc_final: 0.8209 (m) REVERT: C 41 TYR cc_start: 0.6663 (p90) cc_final: 0.6140 (p90) REVERT: C 76 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7623 (p) REVERT: D 93 ASP cc_start: 0.8108 (m-30) cc_final: 0.7651 (m-30) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 1.0928 time to fit residues: 144.1221 Evaluate side-chains 121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 109 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN D 44 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125224 restraints weight = 35265.294| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.09 r_work: 0.3214 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12071 Z= 0.138 Angle : 0.496 7.501 16405 Z= 0.263 Chirality : 0.043 0.142 1783 Planarity : 0.004 0.059 2158 Dihedral : 4.164 16.864 1651 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.50 % Allowed : 10.69 % Favored : 87.81 % 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: 0.18 (0.22), residues: 1487 helix: 2.29 (0.28), residues: 330 sheet: 0.23 (0.25), residues: 443 loop : -1.00 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 583 TYR 0.009 0.001 TYR D 184 PHE 0.016 0.001 PHE A 426 TRP 0.010 0.001 TRP B 143 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00329 (12068) covalent geometry : angle 0.49544 (16403) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.29258 ( 2) hydrogen bonds : bond 0.04175 ( 521) hydrogen bonds : angle 4.41896 ( 1467) Misc. bond : bond 0.00381 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8348 (p0) cc_final: 0.8135 (p0) REVERT: A 286 GLN cc_start: 0.7296 (mp10) cc_final: 0.6385 (tm130) REVERT: A 520 ASN cc_start: 0.8026 (t0) cc_final: 0.7474 (t0) REVERT: A 521 GLU cc_start: 0.7327 (tt0) cc_final: 0.7101 (pt0) REVERT: A 614 ASP cc_start: 0.8307 (m-30) cc_final: 0.8030 (m-30) REVERT: B 268 THR cc_start: 0.8454 (t) cc_final: 0.8210 (m) REVERT: C 41 TYR cc_start: 0.6652 (p90) cc_final: 0.6110 (p90) REVERT: C 76 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7599 (p) REVERT: D 93 ASP cc_start: 0.8103 (m-30) cc_final: 0.7645 (m-30) outliers start: 19 outliers final: 15 residues processed: 122 average time/residue: 1.0952 time to fit residues: 146.6396 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125284 restraints weight = 35269.161| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.11 r_work: 0.3225 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12071 Z= 0.127 Angle : 0.490 7.663 16405 Z= 0.260 Chirality : 0.043 0.140 1783 Planarity : 0.004 0.065 2158 Dihedral : 4.121 16.940 1651 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.35 % Allowed : 11.24 % Favored : 87.41 % 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: 0.25 (0.22), residues: 1487 helix: 2.40 (0.28), residues: 331 sheet: 0.25 (0.25), residues: 443 loop : -0.98 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 583 TYR 0.013 0.001 TYR D 79 PHE 0.016 0.001 PHE A 426 TRP 0.011 0.001 TRP B 348 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00301 (12068) covalent geometry : angle 0.48959 (16403) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.27113 ( 2) hydrogen bonds : bond 0.04009 ( 521) hydrogen bonds : angle 4.36983 ( 1467) Misc. bond : bond 0.00371 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8345 (p0) cc_final: 0.8144 (p0) REVERT: A 286 GLN cc_start: 0.7273 (mp10) cc_final: 0.6381 (tm130) REVERT: A 520 ASN cc_start: 0.8025 (t0) cc_final: 0.7474 (t0) REVERT: A 521 GLU cc_start: 0.7279 (tt0) cc_final: 0.7014 (pt0) REVERT: A 614 ASP cc_start: 0.8303 (m-30) cc_final: 0.8030 (m-30) REVERT: B 41 GLN cc_start: 0.7416 (tm-30) cc_final: 0.6945 (mt0) REVERT: B 268 THR cc_start: 0.8464 (t) cc_final: 0.8227 (m) REVERT: C 41 TYR cc_start: 0.6639 (p90) cc_final: 0.6134 (p90) REVERT: C 76 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7587 (p) REVERT: D 93 ASP cc_start: 0.8105 (m-30) cc_final: 0.7650 (m-30) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 1.0544 time to fit residues: 137.3108 Evaluate side-chains 124 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125148 restraints weight = 35243.057| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.13 r_work: 0.3228 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12071 Z= 0.116 Angle : 0.478 7.795 16405 Z= 0.253 Chirality : 0.042 0.139 1783 Planarity : 0.004 0.071 2158 Dihedral : 4.046 17.040 1651 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.27 % Allowed : 11.32 % Favored : 87.41 % 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: 0.33 (0.22), residues: 1487 helix: 2.53 (0.29), residues: 331 sheet: 0.28 (0.25), residues: 443 loop : -0.95 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 583 TYR 0.011 0.001 TYR D 79 PHE 0.016 0.001 PHE A 426 TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00271 (12068) covalent geometry : angle 0.47741 (16403) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.22753 ( 2) hydrogen bonds : bond 0.03827 ( 521) hydrogen bonds : angle 4.31925 ( 1467) Misc. bond : bond 0.00369 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2974 Ramachandran restraints generated. 1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 286 GLN cc_start: 0.7254 (mp10) cc_final: 0.6370 (tm130) REVERT: A 520 ASN cc_start: 0.8056 (t0) cc_final: 0.7535 (t0) REVERT: A 521 GLU cc_start: 0.7297 (tt0) cc_final: 0.7047 (pt0) REVERT: A 614 ASP cc_start: 0.8359 (m-30) cc_final: 0.8045 (m-30) REVERT: B 41 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6960 (mt0) REVERT: B 268 THR cc_start: 0.8467 (t) cc_final: 0.8236 (m) REVERT: C 41 TYR cc_start: 0.6618 (p90) cc_final: 0.6110 (p90) REVERT: D 93 ASP cc_start: 0.8114 (m-30) cc_final: 0.7657 (m-30) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 1.1008 time to fit residues: 145.2708 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 37 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 135 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125092 restraints weight = 35115.530| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.09 r_work: 0.3233 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12071 Z= 0.105 Angle : 0.472 7.903 16405 Z= 0.250 Chirality : 0.042 0.138 1783 Planarity : 0.004 0.070 2158 Dihedral : 3.999 16.870 1651 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.11 % Allowed : 11.72 % Favored : 87.17 % 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: 0.40 (0.22), residues: 1487 helix: 2.62 (0.29), residues: 331 sheet: 0.32 (0.24), residues: 445 loop : -0.93 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 583 TYR 0.011 0.001 TYR D 79 PHE 0.016 0.001 PHE A 426 TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00244 (12068) covalent geometry : angle 0.47225 (16403) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.18344 ( 2) hydrogen bonds : bond 0.03688 ( 521) hydrogen bonds : angle 4.27080 ( 1467) Misc. bond : bond 0.00359 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6867.15 seconds wall clock time: 116 minutes 34.63 seconds (6994.63 seconds total)