Starting phenix.real_space_refine on Thu Jul 2 20:15:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtj_14142/07_2026/7qtj_14142.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 42 5.16 5 C 6285 2.51 5 N 1673 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9942 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1637 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.55, per 1000 atoms: 0.16 Number of scatterers: 9942 At special positions: 0 Unit cell: (82.998, 161.846, 152.163, 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 42 16.00 O 1942 8.00 N 1673 7.00 C 6285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 331 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 244.5 milliseconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 26 sheets defined 9.8% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.043A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.741A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.529A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.083A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.414A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.838A pdb=" N VAL A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.897A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.196A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.900A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.571A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.666A pdb=" N LEU B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.550A pdb=" N LYS B 98 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.567A pdb=" N PHE B 134 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 153 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.624A pdb=" N SER B 165 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 208 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.898A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.325A pdb=" N LEU C 11 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.844A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.171A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 192 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 194 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.913A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.776A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 396 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 514 " --> pdb=" O TYR D 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.793A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.282A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.386A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 165 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.449A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.182A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164 334 hydrogen bonds defined for protein. 822 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: 1.03 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2750 1.33 - 1.45: 1966 1.45 - 1.58: 5425 1.58 - 1.70: 1 1.70 - 1.82: 47 Bond restraints: 10189 Sorted by residual: bond pdb=" CG PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.503 1.299 0.204 3.40e-02 8.65e+02 3.59e+01 bond pdb=" CA SER B 52 " pdb=" CB SER B 52 " ideal model delta sigma weight residual 1.531 1.464 0.066 1.48e-02 4.57e+03 2.00e+01 bond pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" CB PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.37e+00 bond pdb=" CA SER B 55 " pdb=" CB SER B 55 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.48e-02 4.57e+03 8.97e+00 ... (remaining 10184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 13784 3.92 - 7.83: 66 7.83 - 11.75: 3 11.75 - 15.67: 3 15.67 - 19.59: 1 Bond angle restraints: 13857 Sorted by residual: angle pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 112.00 96.57 15.43 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 92.41 19.59 2.20e+00 2.07e-01 7.93e+01 angle pdb=" N PRO E 121 " pdb=" CD PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 103.20 90.73 12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 111.85 99.84 12.01 1.47e+00 4.63e-01 6.68e+01 angle pdb=" C THR C 172 " pdb=" CA THR C 172 " pdb=" CB THR C 172 " ideal model delta sigma weight residual 114.40 106.53 7.87 1.25e+00 6.40e-01 3.97e+01 ... (remaining 13852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5470 17.93 - 35.86: 451 35.86 - 53.79: 86 53.79 - 71.72: 20 71.72 - 89.65: 9 Dihedral angle restraints: 6036 sinusoidal: 2328 harmonic: 3708 Sorted by residual: dihedral pdb=" CB CYS B 152 " pdb=" SG CYS B 152 " pdb=" SG CYS B 208 " pdb=" CB CYS B 208 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C PHE A 377 " pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta harmonic sigma weight residual -122.60 -107.54 -15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -131.63 45.63 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1416 0.091 - 0.181: 110 0.181 - 0.272: 9 0.272 - 0.362: 3 0.362 - 0.453: 2 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA ARG A 346 " pdb=" N ARG A 346 " pdb=" C ARG A 346 " pdb=" CB ARG A 346 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ARG B 72 " pdb=" N ARG B 72 " pdb=" C ARG B 72 " pdb=" CB ARG B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1537 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 120 " -0.100 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO E 121 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 101 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C HIS B 101 " 0.076 2.00e-02 2.50e+03 pdb=" O HIS B 101 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR B 102 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE B 51 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE B 51 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 52 " 0.024 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 246 2.70 - 3.25: 9271 3.25 - 3.80: 14986 3.80 - 4.35: 19152 4.35 - 4.90: 31923 Nonbonded interactions: 75578 Sorted by model distance: nonbonded pdb=" CB ARG A 346 " pdb=" NE ARG A 346 " model vdw 2.144 2.816 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 102 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 197 " pdb=" OG SER B 200 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG D 403 " pdb=" O GLY D 504 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU B 6 " pdb=" N GLY B 118 " model vdw 2.315 3.120 ... (remaining 75573 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 'A' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.004 0.204 10212 Z= 0.211 Angle : 0.748 19.587 13908 Z= 0.425 Chirality : 0.050 0.453 1540 Planarity : 0.005 0.137 1780 Dihedral : 13.804 89.654 3616 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 1.27 % Allowed : 0.54 % Favored : 98.19 % Cbeta Deviations : 0.34 % 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 (0.25), residues: 1268 helix: -2.11 (0.56), residues: 62 sheet: 1.33 (0.25), residues: 440 loop : -0.43 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 38 TYR 0.025 0.001 TYR B 102 PHE 0.029 0.001 PHE A 377 TRP 0.008 0.001 TRP C 148 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (10189) covalent geometry : angle 0.72749 / 0.42 (13857) SS BOND : bond 0.00271 / 0.16 ( 18) SS BOND : angle 0.62747 / 0.40 ( 36) hydrogen bonds : bond 0.17777 / 12.03 ( 297) hydrogen bonds : angle 6.97827 / 4.95 ( 822) link_BETA1-4 : bond 0.00302 / 0.15 ( 3) link_BETA1-4 : angle 3.95648 / 2.06 ( 9) link_NAG-ASN : bond 0.01025 / 0.54 ( 2) link_NAG-ASN : angle 7.03297 / 3.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ASP cc_start: 0.8876 (m-30) cc_final: 0.8605 (m-30) REVERT: A 375 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6655 (p90) REVERT: D 375 PHE cc_start: 0.5919 (m-10) cc_final: 0.5478 (m-80) REVERT: F 10 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7425 (mm-30) outliers start: 14 outliers final: 4 residues processed: 131 average time/residue: 0.0845 time to fit residues: 15.5437 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN E 91 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099735 restraints weight = 35877.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100121 restraints weight = 33613.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100537 restraints weight = 30441.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.102512 restraints weight = 22016.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102497 restraints weight = 15987.247| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10212 Z= 0.119 Angle : 0.619 14.240 13908 Z= 0.309 Chirality : 0.045 0.332 1540 Planarity : 0.004 0.052 1780 Dihedral : 3.758 21.754 1394 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1268 helix: -2.18 (0.55), residues: 60 sheet: 1.27 (0.25), residues: 458 loop : -0.43 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 38 TYR 0.015 0.001 TYR B 102 PHE 0.017 0.001 PHE D 429 TRP 0.014 0.001 TRP B 53 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10189) covalent geometry : angle 0.58780 / 0.30 (13857) SS BOND : bond 0.00756 / 0.35 ( 18) SS BOND : angle 2.25046 / 1.73 ( 36) hydrogen bonds : bond 0.03575 / 2.42 ( 297) hydrogen bonds : angle 5.57522 / 3.94 ( 822) link_BETA1-4 : bond 0.00545 / 0.27 ( 3) link_BETA1-4 : angle 3.46443 / 1.82 ( 9) link_NAG-ASN : bond 0.01073 / 0.56 ( 2) link_NAG-ASN : angle 6.41962 / 3.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8460 (p0) cc_final: 0.8174 (p0) REVERT: A 389 ASP cc_start: 0.9209 (p0) cc_final: 0.8608 (p0) REVERT: A 392 PHE cc_start: 0.8006 (m-80) cc_final: 0.7757 (m-80) REVERT: D 375 PHE cc_start: 0.5724 (m-10) cc_final: 0.5499 (m-80) outliers start: 3 outliers final: 0 residues processed: 126 average time/residue: 0.0821 time to fit residues: 14.7962 Evaluate side-chains 82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 5 optimal weight: 0.0010 chunk 125 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 67 optimal weight: 0.0980 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 ASN C 138 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.114058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094608 restraints weight = 35912.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.094753 restraints weight = 40969.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095409 restraints weight = 37634.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.095972 restraints weight = 25080.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096515 restraints weight = 21541.082| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10212 Z= 0.234 Angle : 0.726 14.203 13908 Z= 0.370 Chirality : 0.047 0.244 1540 Planarity : 0.005 0.040 1780 Dihedral : 4.571 22.238 1394 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.23 % Favored : 93.53 % Rotamer: Outliers : 0.27 % Allowed : 5.90 % Favored : 93.83 % 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: -0.37 (0.24), residues: 1268 helix: -2.30 (0.57), residues: 61 sheet: 0.66 (0.24), residues: 472 loop : -0.66 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.019 0.002 TYR B 102 PHE 0.021 0.002 PHE B 158 TRP 0.028 0.002 TRP A 436 HIS 0.006 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (10189) covalent geometry : angle 0.69834 / 0.36 (13857) SS BOND : bond 0.00657 / 0.35 ( 18) SS BOND : angle 2.33189 / 1.76 ( 36) hydrogen bonds : bond 0.04004 / 2.75 ( 297) hydrogen bonds : angle 5.75234 / 4.04 ( 822) link_BETA1-4 : bond 0.00347 / 0.17 ( 3) link_BETA1-4 : angle 3.66516 / 1.97 ( 9) link_NAG-ASN : bond 0.00928 / 0.49 ( 2) link_NAG-ASN : angle 6.62426 / 3.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8766 (t70) cc_final: 0.8388 (t0) REVERT: C 194 CYS cc_start: 0.0118 (p) cc_final: -0.0477 (p) REVERT: A 389 ASP cc_start: 0.9282 (p0) cc_final: 0.8725 (p0) REVERT: A 392 PHE cc_start: 0.8229 (m-80) cc_final: 0.7924 (m-80) REVERT: A 406 GLU cc_start: 0.8893 (mp0) cc_final: 0.8621 (mm-30) outliers start: 3 outliers final: 1 residues processed: 113 average time/residue: 0.1127 time to fit residues: 17.6261 Evaluate side-chains 79 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.118730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.102607 restraints weight = 37846.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102000 restraints weight = 51952.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.102963 restraints weight = 44807.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.103372 restraints weight = 28722.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.104063 restraints weight = 24842.202| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10212 Z= 0.113 Angle : 0.625 13.676 13908 Z= 0.313 Chirality : 0.045 0.270 1540 Planarity : 0.004 0.036 1780 Dihedral : 4.237 22.757 1394 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 0.18 % Allowed : 3.54 % Favored : 96.28 % 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: -0.21 (0.24), residues: 1268 helix: -2.34 (0.56), residues: 60 sheet: 0.82 (0.24), residues: 478 loop : -0.59 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.015 0.001 TYR B 102 PHE 0.029 0.001 PHE C 71 TRP 0.015 0.001 TRP A 436 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10189) covalent geometry : angle 0.59915 / 0.31 (13857) SS BOND : bond 0.00521 / 0.29 ( 18) SS BOND : angle 1.79368 / 1.38 ( 36) hydrogen bonds : bond 0.03114 / 2.09 ( 297) hydrogen bonds : angle 5.45425 / 3.79 ( 822) link_BETA1-4 : bond 0.00557 / 0.28 ( 3) link_BETA1-4 : angle 3.54121 / 1.89 ( 9) link_NAG-ASN : bond 0.01180 / 0.62 ( 2) link_NAG-ASN : angle 6.29660 / 3.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8536 (p0) cc_final: 0.8292 (p0) REVERT: B 99 ASP cc_start: 0.8721 (t70) cc_final: 0.8217 (t0) REVERT: C 14 SER cc_start: 0.8627 (p) cc_final: 0.8373 (m) REVERT: C 145 LYS cc_start: 0.8432 (tppt) cc_final: 0.8190 (tppt) REVERT: C 194 CYS cc_start: 0.0019 (p) cc_final: -0.0771 (p) REVERT: A 389 ASP cc_start: 0.9258 (p0) cc_final: 0.8733 (p0) REVERT: A 392 PHE cc_start: 0.8096 (m-80) cc_final: 0.7766 (m-80) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.1162 time to fit residues: 20.0722 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092294 restraints weight = 36269.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.093082 restraints weight = 40654.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093649 restraints weight = 35003.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094049 restraints weight = 23493.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094734 restraints weight = 20377.797| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10212 Z= 0.284 Angle : 0.791 14.333 13908 Z= 0.405 Chirality : 0.050 0.309 1540 Planarity : 0.006 0.060 1780 Dihedral : 5.106 22.709 1394 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.10 % Favored : 92.67 % Rotamer: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % 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: -0.72 (0.24), residues: 1268 helix: -2.54 (0.57), residues: 61 sheet: 0.37 (0.24), residues: 484 loop : -0.88 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 108 TYR 0.023 0.003 TYR C 87 PHE 0.035 0.002 PHE C 71 TRP 0.037 0.003 TRP A 436 HIS 0.009 0.002 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (10189) covalent geometry : angle 0.76155 / 0.40 (13857) SS BOND : bond 0.01062 / 0.52 ( 18) SS BOND : angle 2.69921 / 2.03 ( 36) hydrogen bonds : bond 0.04266 / 2.94 ( 297) hydrogen bonds : angle 5.98588 / 4.18 ( 822) link_BETA1-4 : bond 0.00378 / 0.19 ( 3) link_BETA1-4 : angle 3.76440 / 2.02 ( 9) link_NAG-ASN : bond 0.00927 / 0.48 ( 2) link_NAG-ASN : angle 6.77924 / 3.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8886 (t70) cc_final: 0.8258 (t0) REVERT: C 14 SER cc_start: 0.8824 (p) cc_final: 0.8569 (m) REVERT: C 194 CYS cc_start: 0.0193 (p) cc_final: -0.0546 (p) REVERT: A 389 ASP cc_start: 0.9163 (p0) cc_final: 0.8682 (p0) REVERT: A 392 PHE cc_start: 0.8032 (m-80) cc_final: 0.7656 (m-80) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1158 time to fit residues: 15.7406 Evaluate side-chains 73 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.0170 chunk 75 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 overall best weight: 3.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.111832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092119 restraints weight = 35988.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.092851 restraints weight = 34560.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093047 restraints weight = 36006.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093805 restraints weight = 22034.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094113 restraints weight = 18470.262| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10212 Z= 0.231 Angle : 0.757 14.701 13908 Z= 0.384 Chirality : 0.049 0.343 1540 Planarity : 0.005 0.050 1780 Dihedral : 5.186 24.324 1394 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.07 % Favored : 93.69 % Rotamer: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % 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: -1.00 (0.23), residues: 1268 helix: -2.74 (0.53), residues: 67 sheet: 0.18 (0.24), residues: 482 loop : -1.05 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 61 TYR 0.031 0.002 TYR B 94 PHE 0.027 0.002 PHE C 71 TRP 0.036 0.002 TRP A 436 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (10189) covalent geometry : angle 0.72758 / 0.38 (13857) SS BOND : bond 0.00786 / 0.39 ( 18) SS BOND : angle 2.50910 / 1.89 ( 36) hydrogen bonds : bond 0.03897 / 2.69 ( 297) hydrogen bonds : angle 5.99064 / 4.16 ( 822) link_BETA1-4 : bond 0.00511 / 0.25 ( 3) link_BETA1-4 : angle 3.69208 / 1.99 ( 9) link_NAG-ASN : bond 0.00990 / 0.52 ( 2) link_NAG-ASN : angle 6.86031 / 3.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8850 (t70) cc_final: 0.8357 (t0) REVERT: C 14 SER cc_start: 0.8856 (p) cc_final: 0.8647 (m) REVERT: C 145 LYS cc_start: 0.8627 (tppt) cc_final: 0.8405 (tppt) REVERT: C 194 CYS cc_start: 0.0244 (p) cc_final: -0.0465 (p) REVERT: A 389 ASP cc_start: 0.9294 (p0) cc_final: 0.8848 (p0) REVERT: A 392 PHE cc_start: 0.8073 (m-80) cc_final: 0.7612 (m-80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1177 time to fit residues: 16.2170 Evaluate side-chains 74 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.111913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092334 restraints weight = 35644.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092954 restraints weight = 41160.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093400 restraints weight = 37022.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.094073 restraints weight = 23656.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094632 restraints weight = 20433.584| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10212 Z= 0.212 Angle : 0.737 14.886 13908 Z= 0.374 Chirality : 0.048 0.289 1540 Planarity : 0.005 0.040 1780 Dihedral : 5.189 24.374 1394 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.94 % Favored : 92.82 % Rotamer: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % 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: -1.12 (0.23), residues: 1268 helix: -2.74 (0.53), residues: 67 sheet: 0.05 (0.24), residues: 483 loop : -1.10 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 222 TYR 0.022 0.002 TYR B 94 PHE 0.024 0.002 PHE C 71 TRP 0.031 0.002 TRP A 436 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (10189) covalent geometry : angle 0.70880 / 0.37 (13857) SS BOND : bond 0.00720 / 0.38 ( 18) SS BOND : angle 2.26522 / 1.69 ( 36) hydrogen bonds : bond 0.03764 / 2.60 ( 297) hydrogen bonds : angle 5.89525 / 4.11 ( 822) link_BETA1-4 : bond 0.00512 / 0.26 ( 3) link_BETA1-4 : angle 3.67093 / 1.98 ( 9) link_NAG-ASN : bond 0.01049 / 0.55 ( 2) link_NAG-ASN : angle 6.90014 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8831 (t70) cc_final: 0.8323 (t0) REVERT: C 14 SER cc_start: 0.8793 (p) cc_final: 0.8570 (m) REVERT: C 194 CYS cc_start: -0.0233 (p) cc_final: -0.0665 (p) REVERT: A 389 ASP cc_start: 0.9242 (p0) cc_final: 0.8764 (p0) REVERT: D 429 PHE cc_start: 0.7291 (t80) cc_final: 0.6532 (t80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1227 time to fit residues: 16.7840 Evaluate side-chains 76 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.1980 chunk 14 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 chunk 110 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.114346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094833 restraints weight = 35526.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095841 restraints weight = 37076.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096336 restraints weight = 31250.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096863 restraints weight = 21003.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097153 restraints weight = 18732.832| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10212 Z= 0.120 Angle : 0.696 14.548 13908 Z= 0.346 Chirality : 0.047 0.302 1540 Planarity : 0.004 0.036 1780 Dihedral : 4.857 27.178 1394 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % 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: -0.83 (0.24), residues: 1268 helix: -2.48 (0.58), residues: 61 sheet: 0.27 (0.24), residues: 470 loop : -0.92 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 222 TYR 0.021 0.001 TYR E 33 PHE 0.021 0.001 PHE C 71 TRP 0.019 0.001 TRP A 436 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10189) covalent geometry : angle 0.66625 / 0.34 (13857) SS BOND : bond 0.00708 / 0.33 ( 18) SS BOND : angle 2.39155 / 1.84 ( 36) hydrogen bonds : bond 0.03318 / 2.24 ( 297) hydrogen bonds : angle 5.66791 / 3.95 ( 822) link_BETA1-4 : bond 0.00634 / 0.32 ( 3) link_BETA1-4 : angle 3.49181 / 1.88 ( 9) link_NAG-ASN : bond 0.01223 / 0.64 ( 2) link_NAG-ASN : angle 6.64911 / 3.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8773 (t70) cc_final: 0.8413 (t0) REVERT: C 14 SER cc_start: 0.8713 (p) cc_final: 0.8432 (m) REVERT: C 140 TYR cc_start: 0.6964 (t80) cc_final: 0.6610 (t80) REVERT: C 194 CYS cc_start: -0.0374 (p) cc_final: -0.0858 (p) REVERT: A 389 ASP cc_start: 0.9260 (p0) cc_final: 0.8722 (p0) REVERT: E 87 TYR cc_start: 0.8492 (m-80) cc_final: 0.8142 (m-80) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1122 time to fit residues: 17.4936 Evaluate side-chains 82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.114731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.095114 restraints weight = 35349.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096180 restraints weight = 37730.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096541 restraints weight = 29848.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098655 restraints weight = 21436.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098577 restraints weight = 14654.178| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10212 Z= 0.125 Angle : 0.665 14.418 13908 Z= 0.331 Chirality : 0.046 0.297 1540 Planarity : 0.004 0.036 1780 Dihedral : 4.663 26.323 1394 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.24), residues: 1268 helix: -2.53 (0.56), residues: 61 sheet: 0.32 (0.24), residues: 469 loop : -0.88 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.013 0.001 TYR B 102 PHE 0.025 0.001 PHE D 429 TRP 0.019 0.001 TRP A 436 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10189) covalent geometry : angle 0.63664 / 0.32 (13857) SS BOND : bond 0.00493 / 0.28 ( 18) SS BOND : angle 2.11862 / 1.63 ( 36) hydrogen bonds : bond 0.03189 / 2.21 ( 297) hydrogen bonds : angle 5.44430 / 3.80 ( 822) link_BETA1-4 : bond 0.00598 / 0.30 ( 3) link_BETA1-4 : angle 3.47365 / 1.86 ( 9) link_NAG-ASN : bond 0.01175 / 0.62 ( 2) link_NAG-ASN : angle 6.58436 / 3.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8564 (p0) cc_final: 0.8309 (p0) REVERT: B 99 ASP cc_start: 0.8765 (t70) cc_final: 0.8390 (t0) REVERT: C 14 SER cc_start: 0.8690 (p) cc_final: 0.8422 (m) REVERT: C 140 TYR cc_start: 0.6948 (t80) cc_final: 0.6618 (t80) REVERT: C 145 LYS cc_start: 0.8478 (tppt) cc_final: 0.8143 (tppt) REVERT: C 194 CYS cc_start: -0.0404 (p) cc_final: -0.0878 (p) REVERT: A 389 ASP cc_start: 0.9222 (p0) cc_final: 0.8698 (p0) REVERT: E 87 TYR cc_start: 0.8557 (m-80) cc_final: 0.8186 (m-80) REVERT: F 10 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7251 (mm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1073 time to fit residues: 16.9237 Evaluate side-chains 87 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.113028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.093876 restraints weight = 35355.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094092 restraints weight = 39162.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.094457 restraints weight = 39068.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095132 restraints weight = 24257.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.095453 restraints weight = 20473.546| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10212 Z= 0.185 Angle : 0.717 14.714 13908 Z= 0.360 Chirality : 0.047 0.287 1540 Planarity : 0.004 0.045 1780 Dihedral : 4.953 28.744 1394 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.39 % Favored : 93.38 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % 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: -0.96 (0.24), residues: 1268 helix: -2.64 (0.53), residues: 67 sheet: 0.19 (0.24), residues: 469 loop : -0.99 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.019 0.002 TYR F 155 PHE 0.021 0.002 PHE C 71 TRP 0.027 0.002 TRP A 436 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (10189) covalent geometry : angle 0.68980 / 0.35 (13857) SS BOND : bond 0.00726 / 0.35 ( 18) SS BOND : angle 2.18753 / 1.67 ( 36) hydrogen bonds : bond 0.03604 / 2.48 ( 297) hydrogen bonds : angle 5.70240 / 4.00 ( 822) link_BETA1-4 : bond 0.00588 / 0.29 ( 3) link_BETA1-4 : angle 3.55097 / 1.91 ( 9) link_NAG-ASN : bond 0.01107 / 0.58 ( 2) link_NAG-ASN : angle 6.72988 / 3.79 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8598 (p0) cc_final: 0.8278 (p0) REVERT: B 99 ASP cc_start: 0.8849 (t70) cc_final: 0.8459 (t0) REVERT: C 14 SER cc_start: 0.8778 (p) cc_final: 0.8524 (m) REVERT: C 94 TYR cc_start: 0.7914 (t80) cc_final: 0.7630 (t80) REVERT: C 140 TYR cc_start: 0.7024 (t80) cc_final: 0.6680 (t80) REVERT: C 194 CYS cc_start: -0.0285 (p) cc_final: -0.0791 (p) REVERT: A 389 ASP cc_start: 0.9219 (p0) cc_final: 0.8701 (p0) REVERT: D 375 PHE cc_start: 0.5440 (m-80) cc_final: 0.5220 (m-80) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1203 time to fit residues: 16.9884 Evaluate side-chains 81 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 110 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.112896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.093119 restraints weight = 35674.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094629 restraints weight = 34923.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.095048 restraints weight = 27983.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.095383 restraints weight = 19830.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095678 restraints weight = 17758.201| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10212 Z= 0.182 Angle : 0.706 14.817 13908 Z= 0.355 Chirality : 0.046 0.289 1540 Planarity : 0.004 0.037 1780 Dihedral : 4.987 28.818 1394 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.31 % Favored : 93.45 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % 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: -1.06 (0.24), residues: 1268 helix: -2.63 (0.54), residues: 67 sheet: 0.11 (0.24), residues: 469 loop : -1.07 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 222 TYR 0.017 0.002 TYR B 94 PHE 0.026 0.002 PHE D 429 TRP 0.026 0.002 TRP A 436 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (10189) covalent geometry : angle 0.67762 / 0.35 (13857) SS BOND : bond 0.00614 / 0.33 ( 18) SS BOND : angle 2.20099 / 1.66 ( 36) hydrogen bonds : bond 0.03531 / 2.44 ( 297) hydrogen bonds : angle 5.66243 / 3.96 ( 822) link_BETA1-4 : bond 0.00650 / 0.32 ( 3) link_BETA1-4 : angle 3.55354 / 1.92 ( 9) link_NAG-ASN : bond 0.01118 / 0.59 ( 2) link_NAG-ASN : angle 6.76278 / 3.81 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.59 seconds wall clock time: 27 minutes 18.53 seconds (1638.53 seconds total)