Starting phenix.real_space_refine on Wed Mar 4 02:17:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qtj_14142/03_2026/7qtj_14142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtj_14142/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtj_14142/03_2026/7qtj_14142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtj_14142/03_2026/7qtj_14142.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtj_14142/03_2026/7qtj_14142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtj_14142/03_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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.24 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: 0.63 Conformation dependent library (CDL) restraints added in 361.3 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: 0.28 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: 1.37 Time building geometry restraints manager: 0.80 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 - 21.98: 5676 21.98 - 43.95: 381 43.95 - 65.93: 51 65.93 - 87.90: 22 87.90 - 109.88: 9 Dihedral angle restraints: 6139 sinusoidal: 2431 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 6136 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: 1.860 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 15.202 109.878 3719 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 covalent geometry : bond 0.00410 (10189) covalent geometry : angle 0.72749 (13857) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.62747 ( 36) hydrogen bonds : bond 0.17777 ( 297) hydrogen bonds : angle 6.97827 ( 822) link_BETA1-4 : bond 0.00302 ( 3) link_BETA1-4 : angle 3.95648 ( 9) link_NAG-ASN : bond 0.01025 ( 2) link_NAG-ASN : angle 7.03297 ( 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 : 0.341 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: 0.1048 time to fit residues: 18.9887 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 : 0.390 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.119555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099759 restraints weight = 35958.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.100104 restraints weight = 33781.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100522 restraints weight = 30960.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.102403 restraints weight = 22342.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.102387 restraints weight = 16707.006| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10212 Z= 0.119 Angle : 0.627 14.536 13908 Z= 0.311 Chirality : 0.045 0.376 1540 Planarity : 0.004 0.053 1780 Dihedral : 8.307 79.121 1497 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.27 % Allowed : 4.99 % Favored : 94.74 % 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 0.016 0.001 PHE D 429 TRP 0.013 0.001 TRP B 53 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00262 (10189) covalent geometry : angle 0.59694 (13857) SS BOND : bond 0.00681 ( 18) SS BOND : angle 2.11201 ( 36) hydrogen bonds : bond 0.03645 ( 297) hydrogen bonds : angle 5.58815 ( 822) link_BETA1-4 : bond 0.00903 ( 3) link_BETA1-4 : angle 3.40503 ( 9) link_NAG-ASN : bond 0.01143 ( 2) link_NAG-ASN : angle 6.65760 ( 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 126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8458 (p0) cc_final: 0.8162 (p0) REVERT: A 389 ASP cc_start: 0.9205 (p0) cc_final: 0.8609 (p0) REVERT: A 392 PHE cc_start: 0.8006 (m-80) cc_final: 0.7750 (m-80) REVERT: D 375 PHE cc_start: 0.5725 (m-10) cc_final: 0.5498 (m-80) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.0995 time to fit residues: 17.5687 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 : 0.299 ------------------------------------------------------------------------------- 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: 8.9990 chunk 114 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 125 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.114804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095423 restraints weight = 35921.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095674 restraints weight = 40482.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096397 restraints weight = 36212.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.096896 restraints weight = 23727.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.097690 restraints weight = 20687.111| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10212 Z= 0.211 Angle : 0.703 14.462 13908 Z= 0.355 Chirality : 0.047 0.225 1540 Planarity : 0.004 0.042 1780 Dihedral : 6.945 56.622 1497 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.52 % Favored : 94.24 % Rotamer: Outliers : 0.36 % Allowed : 5.81 % 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: -0.26 (0.24), residues: 1268 helix: -2.25 (0.57), residues: 60 sheet: 0.75 (0.24), residues: 473 loop : -0.60 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.017 0.002 TYR B 102 PHE 0.019 0.002 PHE B 158 TRP 0.013 0.002 TRP B 53 HIS 0.005 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00472 (10189) covalent geometry : angle 0.67237 (13857) SS BOND : bond 0.00944 ( 18) SS BOND : angle 2.33539 ( 36) hydrogen bonds : bond 0.03833 ( 297) hydrogen bonds : angle 5.61602 ( 822) link_BETA1-4 : bond 0.00837 ( 3) link_BETA1-4 : angle 3.61500 ( 9) link_NAG-ASN : bond 0.00893 ( 2) link_NAG-ASN : angle 6.91577 ( 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 121 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8561 (p0) cc_final: 0.8266 (p0) REVERT: B 99 ASP cc_start: 0.8868 (t0) cc_final: 0.8456 (t0) REVERT: C 194 CYS cc_start: 0.0005 (p) cc_final: -0.0596 (p) REVERT: A 389 ASP cc_start: 0.9255 (p0) cc_final: 0.8715 (p0) REVERT: A 392 PHE cc_start: 0.8189 (m-80) cc_final: 0.7864 (m-80) REVERT: A 406 GLU cc_start: 0.8922 (mp0) cc_final: 0.8681 (mm-30) outliers start: 4 outliers final: 2 residues processed: 120 average time/residue: 0.1124 time to fit residues: 18.4923 Evaluate side-chains 79 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4047 r_free = 0.4047 target = 0.118937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.102823 restraints weight = 37828.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.102490 restraints weight = 52208.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102972 restraints weight = 43881.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.105080 restraints weight = 30788.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.105105 restraints weight = 20146.987| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10212 Z= 0.118 Angle : 0.641 14.094 13908 Z= 0.318 Chirality : 0.045 0.289 1540 Planarity : 0.004 0.036 1780 Dihedral : 6.323 56.983 1497 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % 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: -0.19 (0.24), residues: 1268 helix: -2.29 (0.57), residues: 60 sheet: 0.86 (0.24), residues: 472 loop : -0.59 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.015 0.001 TYR B 102 PHE 0.034 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 covalent geometry : bond 0.00263 (10189) covalent geometry : angle 0.61213 (13857) SS BOND : bond 0.00603 ( 18) SS BOND : angle 1.97365 ( 36) hydrogen bonds : bond 0.03132 ( 297) hydrogen bonds : angle 5.41510 ( 822) link_BETA1-4 : bond 0.00976 ( 3) link_BETA1-4 : angle 3.44887 ( 9) link_NAG-ASN : bond 0.01095 ( 2) link_NAG-ASN : angle 6.66182 ( 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 128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8397 (p0) cc_final: 0.8115 (p0) REVERT: B 99 ASP cc_start: 0.8659 (t0) cc_final: 0.8196 (t0) REVERT: C 14 SER cc_start: 0.8500 (p) cc_final: 0.8169 (m) REVERT: C 194 CYS cc_start: -0.0208 (p) cc_final: -0.1052 (p) REVERT: A 389 ASP cc_start: 0.9084 (p0) cc_final: 0.8454 (p0) REVERT: A 392 PHE cc_start: 0.7949 (m-80) cc_final: 0.7726 (m-80) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1140 time to fit residues: 19.9546 Evaluate side-chains 84 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3941 r_free = 0.3941 target = 0.112966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093399 restraints weight = 36121.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.094902 restraints weight = 38596.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095220 restraints weight = 30781.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096032 restraints weight = 21350.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096278 restraints weight = 18634.782| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10212 Z= 0.241 Angle : 0.748 14.676 13908 Z= 0.380 Chirality : 0.048 0.292 1540 Planarity : 0.005 0.044 1780 Dihedral : 6.370 58.102 1497 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.70 % Favored : 93.06 % Rotamer: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % 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: -0.52 (0.24), residues: 1268 helix: -2.30 (0.62), residues: 55 sheet: 0.51 (0.24), residues: 481 loop : -0.77 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 108 TYR 0.021 0.002 TYR C 87 PHE 0.037 0.002 PHE C 71 TRP 0.013 0.002 TRP A 353 HIS 0.008 0.002 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00548 (10189) covalent geometry : angle 0.71902 (13857) SS BOND : bond 0.00756 ( 18) SS BOND : angle 2.40140 ( 36) hydrogen bonds : bond 0.03969 ( 297) hydrogen bonds : angle 5.78293 ( 822) link_BETA1-4 : bond 0.00785 ( 3) link_BETA1-4 : angle 3.74380 ( 9) link_NAG-ASN : bond 0.00961 ( 2) link_NAG-ASN : angle 6.84551 ( 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 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8735 (t0) cc_final: 0.8256 (t0) REVERT: C 14 SER cc_start: 0.8791 (p) cc_final: 0.8508 (m) REVERT: C 70 GLU cc_start: 0.8521 (tt0) cc_final: 0.8029 (tm-30) REVERT: C 107 GLU cc_start: 0.7508 (tp30) cc_final: 0.7280 (tp30) REVERT: C 194 CYS cc_start: 0.0083 (p) cc_final: -0.0728 (p) REVERT: A 389 ASP cc_start: 0.9169 (p0) cc_final: 0.8669 (p0) REVERT: A 392 PHE cc_start: 0.8092 (m-80) cc_final: 0.7718 (m-80) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.1081 time to fit residues: 15.3240 Evaluate side-chains 77 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.116122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.096192 restraints weight = 35835.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.096643 restraints weight = 33487.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096942 restraints weight = 32271.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.097724 restraints weight = 20969.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.097954 restraints weight = 18021.734| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10212 Z= 0.111 Angle : 0.656 14.123 13908 Z= 0.323 Chirality : 0.045 0.259 1540 Planarity : 0.004 0.035 1780 Dihedral : 5.909 57.224 1497 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 0.09 % Allowed : 2.36 % Favored : 97.55 % 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: -0.41 (0.24), residues: 1268 helix: -2.30 (0.58), residues: 61 sheet: 0.60 (0.24), residues: 478 loop : -0.68 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.014 0.001 TYR B 102 PHE 0.026 0.001 PHE C 71 TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00247 (10189) covalent geometry : angle 0.62644 (13857) SS BOND : bond 0.00528 ( 18) SS BOND : angle 2.16341 ( 36) hydrogen bonds : bond 0.03040 ( 297) hydrogen bonds : angle 5.42309 ( 822) link_BETA1-4 : bond 0.00845 ( 3) link_BETA1-4 : angle 3.52699 ( 9) link_NAG-ASN : bond 0.01204 ( 2) link_NAG-ASN : angle 6.59261 ( 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 116 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8654 (t0) cc_final: 0.8252 (t0) REVERT: C 14 SER cc_start: 0.8772 (p) cc_final: 0.8515 (m) REVERT: C 70 GLU cc_start: 0.8551 (tt0) cc_final: 0.8138 (tm-30) REVERT: C 107 GLU cc_start: 0.7462 (tp30) cc_final: 0.7241 (tp30) REVERT: A 389 ASP cc_start: 0.9250 (p0) cc_final: 0.8797 (p0) REVERT: A 392 PHE cc_start: 0.8182 (m-80) cc_final: 0.7759 (m-80) REVERT: D 454 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7175 (mmm160) REVERT: F 10 GLU cc_start: 0.7716 (tp30) cc_final: 0.7514 (mm-30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1164 time to fit residues: 18.1192 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.085526 restraints weight = 36310.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.084815 restraints weight = 25031.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085196 restraints weight = 22499.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085665 restraints weight = 19812.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.085713 restraints weight = 17879.766| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.076 10212 Z= 0.476 Angle : 1.033 15.694 13908 Z= 0.537 Chirality : 0.057 0.355 1540 Planarity : 0.007 0.061 1780 Dihedral : 7.392 55.477 1497 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.07 % Favored : 90.54 % Rotamer: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % 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: -1.62 (0.23), residues: 1268 helix: -3.01 (0.47), residues: 67 sheet: -0.27 (0.24), residues: 475 loop : -1.46 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.043 0.004 TYR B 94 PHE 0.034 0.004 PHE C 71 TRP 0.050 0.005 TRP F 50 HIS 0.016 0.003 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.01083 (10189) covalent geometry : angle 1.00467 (13857) SS BOND : bond 0.01435 ( 18) SS BOND : angle 3.07456 ( 36) hydrogen bonds : bond 0.05528 ( 297) hydrogen bonds : angle 6.89885 ( 822) link_BETA1-4 : bond 0.00916 ( 3) link_BETA1-4 : angle 4.50336 ( 9) link_NAG-ASN : bond 0.00806 ( 2) link_NAG-ASN : angle 7.30861 ( 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 89 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8855 (t0) cc_final: 0.8406 (t0) REVERT: C 82 ASP cc_start: 0.8726 (m-30) cc_final: 0.8513 (m-30) REVERT: C 107 GLU cc_start: 0.7858 (tp30) cc_final: 0.7656 (tp30) REVERT: A 389 ASP cc_start: 0.9337 (p0) cc_final: 0.8994 (p0) REVERT: A 392 PHE cc_start: 0.8083 (m-80) cc_final: 0.7622 (m-80) REVERT: D 375 PHE cc_start: 0.5113 (m-80) cc_final: 0.4785 (m-80) REVERT: D 436 TRP cc_start: 0.8052 (p90) cc_final: 0.7398 (p-90) REVERT: D 473 TYR cc_start: 0.8099 (t80) cc_final: 0.7897 (t80) REVERT: F 10 GLU cc_start: 0.7899 (tp30) cc_final: 0.7657 (mm-30) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1311 time to fit residues: 15.4341 Evaluate side-chains 66 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.0670 chunk 122 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 450 ASN F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.094527 restraints weight = 35517.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093537 restraints weight = 44852.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094006 restraints weight = 39957.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096180 restraints weight = 26815.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.096138 restraints weight = 17403.678| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10212 Z= 0.140 Angle : 0.740 14.800 13908 Z= 0.372 Chirality : 0.048 0.318 1540 Planarity : 0.004 0.038 1780 Dihedral : 6.440 59.642 1497 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 0.91 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1268 helix: -2.81 (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 0.012 0.001 ARG B 222 TYR 0.020 0.002 TYR A 380 PHE 0.026 0.002 PHE C 71 TRP 0.023 0.002 TRP F 50 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00309 (10189) covalent geometry : angle 0.70855 (13857) SS BOND : bond 0.00823 ( 18) SS BOND : angle 2.56712 ( 36) hydrogen bonds : bond 0.03598 ( 297) hydrogen bonds : angle 6.08797 ( 822) link_BETA1-4 : bond 0.00912 ( 3) link_BETA1-4 : angle 3.89511 ( 9) link_NAG-ASN : bond 0.01164 ( 2) link_NAG-ASN : angle 6.94568 ( 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 116 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8636 (t0) cc_final: 0.8148 (t0) REVERT: C 70 GLU cc_start: 0.8769 (tt0) cc_final: 0.8395 (tm-30) REVERT: C 82 ASP cc_start: 0.8776 (m-30) cc_final: 0.8435 (m-30) REVERT: C 107 GLU cc_start: 0.7462 (tp30) cc_final: 0.7123 (tp30) REVERT: A 389 ASP cc_start: 0.9277 (p0) cc_final: 0.8808 (p0) REVERT: A 392 PHE cc_start: 0.7958 (m-80) cc_final: 0.7504 (m-80) REVERT: F 10 GLU cc_start: 0.7793 (tp30) cc_final: 0.7545 (mm-30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1283 time to fit residues: 19.7862 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 : 0.313 ------------------------------------------------------------------------------- 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: 8.9990 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 450 ASN D 460 ASN F 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.112699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093371 restraints weight = 35859.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094444 restraints weight = 39933.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094658 restraints weight = 33404.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095001 restraints weight = 23258.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097355 restraints weight = 21315.359| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10212 Z= 0.160 Angle : 0.711 14.845 13908 Z= 0.357 Chirality : 0.047 0.266 1540 Planarity : 0.004 0.040 1780 Dihedral : 6.149 57.599 1497 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.55 % Favored : 93.22 % Rotamer: Outliers : 0.09 % Allowed : 0.73 % Favored : 99.18 % 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: -1.15 (0.24), residues: 1268 helix: -2.83 (0.51), residues: 67 sheet: 0.02 (0.24), residues: 476 loop : -1.10 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.016 0.002 TYR A 380 PHE 0.025 0.002 PHE C 71 TRP 0.020 0.002 TRP F 50 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00365 (10189) covalent geometry : angle 0.68098 (13857) SS BOND : bond 0.00589 ( 18) SS BOND : angle 2.26638 ( 36) hydrogen bonds : bond 0.03482 ( 297) hydrogen bonds : angle 5.82299 ( 822) link_BETA1-4 : bond 0.00781 ( 3) link_BETA1-4 : angle 3.88465 ( 9) link_NAG-ASN : bond 0.01099 ( 2) link_NAG-ASN : angle 6.90763 ( 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 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8765 (t0) cc_final: 0.8379 (t0) REVERT: C 14 SER cc_start: 0.8649 (p) cc_final: 0.8384 (m) REVERT: C 70 GLU cc_start: 0.8474 (tt0) cc_final: 0.8210 (tm-30) REVERT: C 194 CYS cc_start: 0.0141 (p) cc_final: -0.0762 (p) REVERT: A 389 ASP cc_start: 0.9188 (p0) cc_final: 0.8698 (p0) REVERT: A 392 PHE cc_start: 0.7924 (m-80) cc_final: 0.7516 (m-80) REVERT: F 10 GLU cc_start: 0.7757 (tp30) cc_final: 0.7524 (mm-30) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.1109 time to fit residues: 15.8634 Evaluate side-chains 78 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.0010 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 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 = 0.3935 r_free = 0.3935 target = 0.112694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093557 restraints weight = 35357.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093393 restraints weight = 39334.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.093810 restraints weight = 42575.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.094714 restraints weight = 25570.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094987 restraints weight = 21205.267| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10212 Z= 0.170 Angle : 0.727 14.865 13908 Z= 0.365 Chirality : 0.047 0.287 1540 Planarity : 0.004 0.042 1780 Dihedral : 6.158 59.285 1497 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.31 % Favored : 93.45 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % 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: -1.21 (0.23), residues: 1268 helix: -2.75 (0.52), residues: 67 sheet: -0.02 (0.24), residues: 481 loop : -1.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.017 0.002 TYR C 94 PHE 0.025 0.002 PHE C 71 TRP 0.022 0.002 TRP F 50 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00385 (10189) covalent geometry : angle 0.69572 (13857) SS BOND : bond 0.00663 ( 18) SS BOND : angle 2.47165 ( 36) hydrogen bonds : bond 0.03540 ( 297) hydrogen bonds : angle 5.78607 ( 822) link_BETA1-4 : bond 0.00775 ( 3) link_BETA1-4 : angle 3.88935 ( 9) link_NAG-ASN : bond 0.01095 ( 2) link_NAG-ASN : angle 6.91522 ( 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 : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8730 (t0) cc_final: 0.8362 (t0) REVERT: C 14 SER cc_start: 0.8723 (p) cc_final: 0.8455 (m) REVERT: C 70 GLU cc_start: 0.8597 (tt0) cc_final: 0.8255 (tm-30) REVERT: C 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8395 (m-30) REVERT: A 389 ASP cc_start: 0.9273 (p0) cc_final: 0.8782 (p0) REVERT: A 392 PHE cc_start: 0.7957 (m-80) cc_final: 0.7510 (m-80) REVERT: D 454 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7392 (mmm-85) REVERT: F 10 GLU cc_start: 0.7804 (tp30) cc_final: 0.7556 (mm-30) REVERT: F 155 TYR cc_start: 0.6576 (p90) cc_final: 0.6172 (p90) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1263 time to fit residues: 17.5638 Evaluate side-chains 78 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 91 GLN F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.091212 restraints weight = 35988.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091855 restraints weight = 35677.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092107 restraints weight = 34620.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093762 restraints weight = 23248.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093770 restraints weight = 16935.329| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10212 Z= 0.239 Angle : 0.775 15.191 13908 Z= 0.392 Chirality : 0.048 0.291 1540 Planarity : 0.005 0.057 1780 Dihedral : 6.396 59.044 1497 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.97 % Favored : 91.80 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1268 helix: -2.87 (0.49), residues: 73 sheet: -0.17 (0.24), residues: 470 loop : -1.28 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.023 0.002 TYR C 94 PHE 0.032 0.002 PHE E 72 TRP 0.027 0.002 TRP F 50 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00544 (10189) covalent geometry : angle 0.74418 (13857) SS BOND : bond 0.00675 ( 18) SS BOND : angle 2.48044 ( 36) hydrogen bonds : bond 0.03938 ( 297) hydrogen bonds : angle 6.00464 ( 822) link_BETA1-4 : bond 0.00795 ( 3) link_BETA1-4 : angle 4.05728 ( 9) link_NAG-ASN : bond 0.01032 ( 2) link_NAG-ASN : angle 7.07772 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.02 seconds wall clock time: 27 minutes 16.30 seconds (1636.30 seconds total)