Starting phenix.real_space_refine on Tue Feb 3 23:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.map" model { file = "/net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxb_71964/02_2026/9pxb_71964.cif" } resolution = 3.2 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= 0.001 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 27 5.16 5 C 4971 2.51 5 N 1256 2.21 5 O 1384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7638 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4192 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 37, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1520 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 855 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" 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 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.47, per 1000 atoms: 0.19 Number of scatterers: 7638 At special positions: 0 Unit cell: (97.37, 130.54, 138.03, 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 27 16.00 O 1384 8.00 N 1256 7.00 C 4971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 641 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 177.4 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 48.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 removed outlier: 4.076A pdb=" N ARG A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 20 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 42 removed outlier: 3.569A pdb=" N ILE A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.864A pdb=" N LYS A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 132 removed outlier: 3.802A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Proline residue: A 118 - end of helix removed outlier: 4.211A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.534A pdb=" N GLU A 145 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 190 through 196 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.603A pdb=" N LEU A 225 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 313 through 337 removed outlier: 3.579A pdb=" N GLY A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 4.375A pdb=" N TYR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.559A pdb=" N LEU A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.785A pdb=" N ARG A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 4.009A pdb=" N ILE A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 451 removed outlier: 3.632A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR A 437 " --> pdb=" O MET A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.578A pdb=" N ARG A 626 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 662 through 669 removed outlier: 3.850A pdb=" N ALA A 666 " --> pdb=" O ASN A 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 52 removed outlier: 3.613A pdb=" N VAL C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 72 through 96 removed outlier: 3.579A pdb=" N CYS C 76 " --> pdb=" O TRP C 72 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 4.137A pdb=" N ASP C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 125 removed outlier: 3.918A pdb=" N VAL C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 removed outlier: 4.094A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 176 removed outlier: 3.957A pdb=" N PHE C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.583A pdb=" N ILE C 195 " --> pdb=" O TRP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.579A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.527A pdb=" N TYR A 234 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 7.643A pdb=" N VAL A 657 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 97 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 659 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS A 99 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU A 661 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 101 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.567A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.599A pdb=" N ARG H 98 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1050 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: 1.36 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2350 1.34 - 1.46: 1297 1.46 - 1.57: 4159 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7842 Sorted by residual: bond pdb=" C GLU A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.37e+00 bond pdb=" C SER A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" CB GLN A 383 " pdb=" CG GLN A 383 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 10432 1.40 - 2.79: 211 2.79 - 4.19: 41 4.19 - 5.59: 18 5.59 - 6.98: 4 Bond angle restraints: 10706 Sorted by residual: angle pdb=" C SER A 389 " pdb=" N TRP A 390 " pdb=" CA TRP A 390 " ideal model delta sigma weight residual 121.54 126.06 -4.52 1.91e+00 2.74e-01 5.59e+00 angle pdb=" C TRP C 145 " pdb=" N TRP C 146 " pdb=" CA TRP C 146 " ideal model delta sigma weight residual 121.58 117.14 4.44 1.95e+00 2.63e-01 5.19e+00 angle pdb=" N GLN A 383 " pdb=" CA GLN A 383 " pdb=" CB GLN A 383 " ideal model delta sigma weight residual 110.16 113.30 -3.14 1.48e+00 4.57e-01 4.50e+00 angle pdb=" CA VAL C 73 " pdb=" C VAL C 73 " pdb=" N PRO C 74 " ideal model delta sigma weight residual 118.88 122.05 -3.17 1.54e+00 4.22e-01 4.24e+00 angle pdb=" CA PRO C 74 " pdb=" C PRO C 74 " pdb=" N PRO C 75 " ideal model delta sigma weight residual 117.93 120.26 -2.33 1.20e+00 6.94e-01 3.77e+00 ... (remaining 10701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 4514 22.73 - 45.46: 234 45.46 - 68.19: 30 68.19 - 90.92: 10 90.92 - 113.65: 3 Dihedral angle restraints: 4791 sinusoidal: 2029 harmonic: 2762 Sorted by residual: dihedral pdb=" C10 CLR C 702 " pdb=" C1 CLR C 702 " pdb=" C2 CLR C 702 " pdb=" C3 CLR C 702 " ideal model delta sinusoidal sigma weight residual -56.83 56.82 -113.65 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 125.33 -32.33 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" C1 CLR C 702 " pdb=" C2 CLR C 702 " pdb=" C3 CLR C 702 " pdb=" C4 CLR C 702 " ideal model delta sinusoidal sigma weight residual 57.41 -51.15 108.56 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 4788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 772 0.029 - 0.058: 298 0.058 - 0.087: 96 0.087 - 0.115: 63 0.115 - 0.144: 9 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA GLN A 383 " pdb=" N GLN A 383 " pdb=" C GLN A 383 " pdb=" CB GLN A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA PRO A 104 " pdb=" N PRO A 104 " pdb=" C PRO A 104 " pdb=" CB PRO A 104 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1235 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 390 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C TRP A 390 " 0.047 2.00e-02 2.50e+03 pdb=" O TRP A 390 " -0.018 2.00e-02 2.50e+03 pdb=" N SER A 391 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 379 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU A 379 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 379 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG A 380 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 173 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 174 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.020 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2009 2.80 - 3.33: 7450 3.33 - 3.85: 12328 3.85 - 4.38: 14182 4.38 - 4.90: 24084 Nonbonded interactions: 60053 Sorted by model distance: nonbonded pdb=" OH TYR A 292 " pdb=" O GLY A 346 " model vdw 2.281 3.040 nonbonded pdb=" O ARG A 631 " pdb=" OG1 THR A 635 " model vdw 2.291 3.040 nonbonded pdb=" O LEU A 20 " pdb=" OG SER A 24 " model vdw 2.292 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP C 149 " pdb=" NH1 ARG C 208 " model vdw 2.310 3.120 ... (remaining 60048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.480 Find NCS groups from input model: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.002 0.039 7847 Z= 0.120 Angle : 0.534 6.983 10718 Z= 0.268 Chirality : 0.039 0.144 1238 Planarity : 0.004 0.036 1325 Dihedral : 14.100 113.650 3004 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.68 (0.29), residues: 940 helix: 1.19 (0.28), residues: 388 sheet: 0.69 (0.41), residues: 175 loop : -0.36 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.012 0.001 TYR A 292 PHE 0.012 0.001 PHE A 185 TRP 0.020 0.001 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7842) covalent geometry : angle 0.53386 (10706) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.55873 ( 6) hydrogen bonds : bond 0.14780 ( 367) hydrogen bonds : angle 5.30348 ( 1050) link_BETA1-4 : bond 0.00114 ( 1) link_BETA1-4 : angle 0.96855 ( 3) link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 1.11970 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7476 (mt0) cc_final: 0.7135 (mm110) REVERT: A 383 GLN cc_start: 0.8084 (mp10) cc_final: 0.7793 (mp10) REVERT: A 420 PHE cc_start: 0.8199 (m-80) cc_final: 0.7865 (m-80) REVERT: A 434 PHE cc_start: 0.7493 (m-80) cc_final: 0.6714 (m-80) REVERT: C 214 GLU cc_start: 0.7241 (tp30) cc_final: 0.6909 (tm-30) REVERT: H 80 TYR cc_start: 0.8138 (m-80) cc_final: 0.7826 (m-80) REVERT: H 90 ASP cc_start: 0.8274 (m-30) cc_final: 0.7981 (m-30) REVERT: L 77 ASN cc_start: 0.8329 (p0) cc_final: 0.8088 (p0) REVERT: L 103 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8627 (ttpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1197 time to fit residues: 26.2081 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 HIS ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.118709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082690 restraints weight = 17230.237| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.08 r_work: 0.3094 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7847 Z= 0.134 Angle : 0.639 9.408 10718 Z= 0.321 Chirality : 0.042 0.190 1238 Planarity : 0.004 0.041 1325 Dihedral : 7.162 69.315 1269 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.72 % Allowed : 9.33 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 940 helix: 0.92 (0.27), residues: 392 sheet: 0.54 (0.41), residues: 171 loop : -0.37 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 103 TYR 0.019 0.001 TYR H 99 PHE 0.020 0.001 PHE C 197 TRP 0.036 0.002 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7842) covalent geometry : angle 0.63797 (10706) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.11618 ( 6) hydrogen bonds : bond 0.04003 ( 367) hydrogen bonds : angle 4.44362 ( 1050) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 1.27662 ( 3) link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 0.65950 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7610 (mt0) cc_final: 0.7269 (mm110) REVERT: A 366 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8909 (mmmt) REVERT: A 420 PHE cc_start: 0.8448 (m-80) cc_final: 0.8161 (m-80) REVERT: A 430 PHE cc_start: 0.8854 (t80) cc_final: 0.8519 (t80) REVERT: A 434 PHE cc_start: 0.7837 (m-80) cc_final: 0.7367 (m-80) REVERT: C 103 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7683 (ttm110) REVERT: C 148 PHE cc_start: 0.8549 (m-10) cc_final: 0.8286 (m-80) REVERT: C 214 GLU cc_start: 0.7291 (tp30) cc_final: 0.6852 (tm-30) REVERT: H 13 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8345 (tpp80) REVERT: H 80 TYR cc_start: 0.8623 (m-80) cc_final: 0.8415 (m-80) REVERT: H 90 ASP cc_start: 0.8879 (m-30) cc_final: 0.8534 (m-30) REVERT: L 17 ASP cc_start: 0.8041 (t0) cc_final: 0.7659 (t0) outliers start: 6 outliers final: 2 residues processed: 137 average time/residue: 0.1105 time to fit residues: 19.3805 Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain C residue 88 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.117034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080546 restraints weight = 17085.418| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.10 r_work: 0.3050 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7847 Z= 0.174 Angle : 0.620 7.520 10718 Z= 0.313 Chirality : 0.043 0.142 1238 Planarity : 0.004 0.046 1325 Dihedral : 6.282 58.599 1269 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.67 % Allowed : 11.48 % Favored : 86.84 % 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: 0.34 (0.28), residues: 940 helix: 0.91 (0.27), residues: 392 sheet: 0.43 (0.40), residues: 171 loop : -0.49 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 53 TYR 0.034 0.002 TYR A 407 PHE 0.014 0.001 PHE A 429 TRP 0.053 0.002 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7842) covalent geometry : angle 0.61916 (10706) SS BOND : bond 0.00668 ( 3) SS BOND : angle 0.84415 ( 6) hydrogen bonds : bond 0.03870 ( 367) hydrogen bonds : angle 4.35977 ( 1050) link_BETA1-4 : bond 0.00025 ( 1) link_BETA1-4 : angle 0.96731 ( 3) link_NAG-ASN : bond 0.00120 ( 1) link_NAG-ASN : angle 1.06244 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7635 (mt0) cc_final: 0.7308 (mm110) REVERT: A 31 LEU cc_start: 0.8861 (mm) cc_final: 0.8623 (tt) REVERT: A 420 PHE cc_start: 0.8399 (m-80) cc_final: 0.8101 (m-80) REVERT: A 430 PHE cc_start: 0.8897 (t80) cc_final: 0.8532 (t80) REVERT: A 434 PHE cc_start: 0.7883 (m-80) cc_final: 0.7291 (m-80) REVERT: C 214 GLU cc_start: 0.7257 (tp30) cc_final: 0.6873 (tm-30) REVERT: H 80 TYR cc_start: 0.8652 (m-80) cc_final: 0.8442 (m-80) REVERT: H 86 LEU cc_start: 0.9485 (mm) cc_final: 0.9261 (mt) REVERT: H 90 ASP cc_start: 0.8916 (m-30) cc_final: 0.8572 (m-30) REVERT: L 8 THR cc_start: 0.8725 (p) cc_final: 0.8516 (p) REVERT: L 17 ASP cc_start: 0.8058 (t0) cc_final: 0.7629 (t0) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.0909 time to fit residues: 15.7086 Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 432 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.117765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081756 restraints weight = 17218.483| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.09 r_work: 0.3070 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7847 Z= 0.129 Angle : 0.610 9.835 10718 Z= 0.306 Chirality : 0.042 0.186 1238 Planarity : 0.004 0.038 1325 Dihedral : 6.136 58.246 1269 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.39 % Allowed : 12.20 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.28), residues: 940 helix: 0.93 (0.27), residues: 390 sheet: 0.47 (0.40), residues: 170 loop : -0.41 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 103 TYR 0.026 0.001 TYR H 99 PHE 0.014 0.001 PHE C 148 TRP 0.036 0.001 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7842) covalent geometry : angle 0.60962 (10706) SS BOND : bond 0.00532 ( 3) SS BOND : angle 0.72040 ( 6) hydrogen bonds : bond 0.03559 ( 367) hydrogen bonds : angle 4.21622 ( 1050) link_BETA1-4 : bond 0.00099 ( 1) link_BETA1-4 : angle 1.06089 ( 3) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 0.87881 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7634 (mt0) cc_final: 0.7287 (mm110) REVERT: A 420 PHE cc_start: 0.8470 (m-80) cc_final: 0.8168 (m-80) REVERT: A 430 PHE cc_start: 0.8900 (t80) cc_final: 0.8574 (t80) REVERT: A 434 PHE cc_start: 0.7959 (m-80) cc_final: 0.7394 (m-80) REVERT: C 56 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7504 (p) REVERT: C 103 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7587 (ttm110) REVERT: C 214 GLU cc_start: 0.7235 (tp30) cc_final: 0.6854 (tm-30) REVERT: H 86 LEU cc_start: 0.9463 (mm) cc_final: 0.9247 (mt) REVERT: H 90 ASP cc_start: 0.8896 (m-30) cc_final: 0.8524 (m-30) REVERT: L 17 ASP cc_start: 0.7993 (t0) cc_final: 0.7490 (t0) outliers start: 20 outliers final: 10 residues processed: 138 average time/residue: 0.0886 time to fit residues: 16.1752 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 88 optimal weight: 0.0010 chunk 76 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.118182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081532 restraints weight = 17154.930| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.14 r_work: 0.3071 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7847 Z= 0.131 Angle : 0.620 8.115 10718 Z= 0.312 Chirality : 0.041 0.163 1238 Planarity : 0.004 0.051 1325 Dihedral : 6.061 57.264 1269 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.39 % Allowed : 14.00 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.28), residues: 940 helix: 0.92 (0.27), residues: 390 sheet: 0.44 (0.41), residues: 170 loop : -0.41 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.027 0.001 TYR H 99 PHE 0.028 0.001 PHE C 148 TRP 0.046 0.002 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7842) covalent geometry : angle 0.61947 (10706) SS BOND : bond 0.00526 ( 3) SS BOND : angle 0.71069 ( 6) hydrogen bonds : bond 0.03540 ( 367) hydrogen bonds : angle 4.18049 ( 1050) link_BETA1-4 : bond 0.00141 ( 1) link_BETA1-4 : angle 1.08555 ( 3) link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 0.88020 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7593 (mt0) cc_final: 0.7241 (mm110) REVERT: A 420 PHE cc_start: 0.8483 (m-80) cc_final: 0.8200 (m-80) REVERT: A 430 PHE cc_start: 0.8843 (t80) cc_final: 0.8497 (t80) REVERT: A 434 PHE cc_start: 0.7928 (m-80) cc_final: 0.7296 (m-80) REVERT: A 447 MET cc_start: 0.8119 (ppp) cc_final: 0.7887 (ptm) REVERT: C 56 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 66 ILE cc_start: 0.6895 (mt) cc_final: 0.6652 (mp) REVERT: C 87 LEU cc_start: 0.7935 (tt) cc_final: 0.7671 (pp) REVERT: C 214 GLU cc_start: 0.7243 (tp30) cc_final: 0.6851 (tm-30) REVERT: H 86 LEU cc_start: 0.9530 (mm) cc_final: 0.9308 (mt) REVERT: H 90 ASP cc_start: 0.8928 (m-30) cc_final: 0.8537 (m-30) REVERT: L 17 ASP cc_start: 0.8053 (t0) cc_final: 0.7613 (t0) outliers start: 20 outliers final: 11 residues processed: 133 average time/residue: 0.0875 time to fit residues: 15.5741 Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.0170 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081281 restraints weight = 17345.967| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.15 r_work: 0.3064 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7847 Z= 0.141 Angle : 0.620 7.439 10718 Z= 0.313 Chirality : 0.042 0.139 1238 Planarity : 0.004 0.039 1325 Dihedral : 6.041 56.782 1269 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 13.40 % Favored : 83.73 % 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: 0.37 (0.28), residues: 940 helix: 0.91 (0.27), residues: 389 sheet: 0.42 (0.41), residues: 170 loop : -0.41 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 103 TYR 0.030 0.001 TYR H 99 PHE 0.030 0.001 PHE C 197 TRP 0.068 0.002 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7842) covalent geometry : angle 0.62018 (10706) SS BOND : bond 0.00533 ( 3) SS BOND : angle 0.64346 ( 6) hydrogen bonds : bond 0.03556 ( 367) hydrogen bonds : angle 4.18111 ( 1050) link_BETA1-4 : bond 0.00160 ( 1) link_BETA1-4 : angle 1.04617 ( 3) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 0.94617 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7588 (mt0) cc_final: 0.7235 (mm110) REVERT: A 366 LYS cc_start: 0.9246 (mmmt) cc_final: 0.9020 (mmmt) REVERT: A 420 PHE cc_start: 0.8496 (m-80) cc_final: 0.8208 (m-80) REVERT: A 447 MET cc_start: 0.8116 (ppp) cc_final: 0.7869 (ptm) REVERT: C 56 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7529 (p) REVERT: C 66 ILE cc_start: 0.6920 (mt) cc_final: 0.6673 (mp) REVERT: C 87 LEU cc_start: 0.7923 (tt) cc_final: 0.7680 (pp) REVERT: C 214 GLU cc_start: 0.7173 (tp30) cc_final: 0.6642 (tm-30) REVERT: H 13 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8139 (tpp80) REVERT: H 86 LEU cc_start: 0.9529 (mm) cc_final: 0.9308 (mt) REVERT: H 90 ASP cc_start: 0.8952 (m-30) cc_final: 0.8530 (m-30) REVERT: L 17 ASP cc_start: 0.8038 (t0) cc_final: 0.7609 (t0) outliers start: 24 outliers final: 13 residues processed: 132 average time/residue: 0.0911 time to fit residues: 15.8309 Evaluate side-chains 131 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.118382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.081737 restraints weight = 17187.423| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.15 r_work: 0.3073 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7847 Z= 0.131 Angle : 0.620 7.219 10718 Z= 0.313 Chirality : 0.041 0.136 1238 Planarity : 0.004 0.044 1325 Dihedral : 5.956 55.410 1269 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.51 % Allowed : 14.83 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.28), residues: 940 helix: 0.96 (0.27), residues: 392 sheet: 0.40 (0.41), residues: 170 loop : -0.36 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 103 TYR 0.030 0.001 TYR H 99 PHE 0.030 0.001 PHE C 197 TRP 0.055 0.002 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7842) covalent geometry : angle 0.61993 (10706) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.63565 ( 6) hydrogen bonds : bond 0.03511 ( 367) hydrogen bonds : angle 4.11942 ( 1050) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.02776 ( 3) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 0.91462 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7595 (mt0) cc_final: 0.7236 (mm110) REVERT: A 407 TYR cc_start: 0.6937 (p90) cc_final: 0.6416 (p90) REVERT: A 420 PHE cc_start: 0.8479 (m-80) cc_final: 0.8191 (m-80) REVERT: A 430 PHE cc_start: 0.8770 (t80) cc_final: 0.8177 (t80) REVERT: A 434 PHE cc_start: 0.7917 (m-80) cc_final: 0.7560 (m-80) REVERT: A 447 MET cc_start: 0.8088 (ppp) cc_final: 0.7623 (ptm) REVERT: C 56 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7522 (p) REVERT: C 66 ILE cc_start: 0.6992 (mt) cc_final: 0.6742 (mp) REVERT: C 87 LEU cc_start: 0.7986 (tt) cc_final: 0.7757 (pp) REVERT: C 148 PHE cc_start: 0.8589 (m-80) cc_final: 0.8376 (m-80) REVERT: C 214 GLU cc_start: 0.7172 (tp30) cc_final: 0.6633 (tm-30) REVERT: L 17 ASP cc_start: 0.8097 (t0) cc_final: 0.7694 (t0) outliers start: 21 outliers final: 13 residues processed: 136 average time/residue: 0.0968 time to fit residues: 17.4083 Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081608 restraints weight = 17242.623| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.16 r_work: 0.3072 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7847 Z= 0.136 Angle : 0.631 7.048 10718 Z= 0.318 Chirality : 0.042 0.239 1238 Planarity : 0.004 0.039 1325 Dihedral : 5.913 54.679 1269 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.39 % Allowed : 15.43 % Favored : 82.18 % 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: 0.46 (0.28), residues: 940 helix: 1.01 (0.27), residues: 392 sheet: 0.38 (0.41), residues: 170 loop : -0.37 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 103 TYR 0.030 0.001 TYR H 99 PHE 0.041 0.001 PHE C 197 TRP 0.041 0.001 TRP C 145 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7842) covalent geometry : angle 0.63111 (10706) SS BOND : bond 0.00512 ( 3) SS BOND : angle 0.63924 ( 6) hydrogen bonds : bond 0.03526 ( 367) hydrogen bonds : angle 4.12058 ( 1050) link_BETA1-4 : bond 0.00165 ( 1) link_BETA1-4 : angle 1.03569 ( 3) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 0.96720 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7579 (mt0) cc_final: 0.7217 (mm110) REVERT: A 366 LYS cc_start: 0.9282 (mmmt) cc_final: 0.9053 (mmmt) REVERT: A 420 PHE cc_start: 0.8483 (m-80) cc_final: 0.8197 (m-80) REVERT: A 430 PHE cc_start: 0.8780 (t80) cc_final: 0.8359 (t80) REVERT: A 434 PHE cc_start: 0.7935 (m-80) cc_final: 0.7564 (m-80) REVERT: A 447 MET cc_start: 0.8137 (ppp) cc_final: 0.7699 (ptm) REVERT: C 56 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7526 (p) REVERT: C 66 ILE cc_start: 0.6999 (mt) cc_final: 0.6745 (mp) REVERT: C 119 ASN cc_start: 0.8914 (m-40) cc_final: 0.8688 (m110) REVERT: C 214 GLU cc_start: 0.7219 (tp30) cc_final: 0.6738 (tm-30) REVERT: H 10 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8053 (mp0) REVERT: H 13 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8280 (tpp80) REVERT: L 17 ASP cc_start: 0.8138 (t0) cc_final: 0.7761 (t0) REVERT: L 105 GLU cc_start: 0.7965 (pm20) cc_final: 0.7367 (pm20) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.0974 time to fit residues: 16.5329 Evaluate side-chains 132 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.115765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079126 restraints weight = 17172.746| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.13 r_work: 0.3019 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7847 Z= 0.228 Angle : 0.697 11.545 10718 Z= 0.350 Chirality : 0.044 0.193 1238 Planarity : 0.005 0.053 1325 Dihedral : 6.233 57.544 1269 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.39 % Allowed : 15.79 % Favored : 81.82 % 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: 0.40 (0.28), residues: 940 helix: 1.05 (0.27), residues: 384 sheet: 0.23 (0.40), residues: 171 loop : -0.42 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 103 TYR 0.036 0.002 TYR H 99 PHE 0.032 0.002 PHE C 148 TRP 0.039 0.002 TRP C 145 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 7842) covalent geometry : angle 0.69612 (10706) SS BOND : bond 0.00738 ( 3) SS BOND : angle 0.79179 ( 6) hydrogen bonds : bond 0.04017 ( 367) hydrogen bonds : angle 4.31194 ( 1050) link_BETA1-4 : bond 0.00098 ( 1) link_BETA1-4 : angle 0.94949 ( 3) link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 1.44602 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7610 (mt0) cc_final: 0.7264 (mm110) REVERT: A 366 LYS cc_start: 0.9259 (mmmt) cc_final: 0.9012 (mmmt) REVERT: A 420 PHE cc_start: 0.8512 (m-80) cc_final: 0.8220 (m-80) REVERT: A 430 PHE cc_start: 0.8801 (t80) cc_final: 0.8394 (t80) REVERT: A 434 PHE cc_start: 0.7951 (m-80) cc_final: 0.7571 (m-80) REVERT: C 56 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7545 (p) REVERT: C 66 ILE cc_start: 0.7006 (mt) cc_final: 0.6749 (mp) REVERT: C 214 GLU cc_start: 0.7356 (tp30) cc_final: 0.6765 (tm-30) REVERT: H 10 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8106 (mp0) REVERT: L 17 ASP cc_start: 0.8247 (t0) cc_final: 0.7827 (t0) REVERT: L 103 LYS cc_start: 0.9171 (ttpp) cc_final: 0.8886 (ttpp) REVERT: L 105 GLU cc_start: 0.7930 (pm20) cc_final: 0.7275 (pm20) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.0906 time to fit residues: 15.6369 Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.117167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080442 restraints weight = 17015.623| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.13 r_work: 0.3045 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7847 Z= 0.160 Angle : 0.685 9.747 10718 Z= 0.343 Chirality : 0.043 0.145 1238 Planarity : 0.004 0.040 1325 Dihedral : 6.156 57.080 1269 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.51 % Allowed : 16.51 % Favored : 80.98 % 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 (0.28), residues: 940 helix: 0.99 (0.27), residues: 383 sheet: 0.27 (0.40), residues: 170 loop : -0.41 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 103 TYR 0.038 0.001 TYR H 99 PHE 0.042 0.001 PHE C 197 TRP 0.037 0.002 TRP C 145 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7842) covalent geometry : angle 0.68493 (10706) SS BOND : bond 0.00583 ( 3) SS BOND : angle 0.73305 ( 6) hydrogen bonds : bond 0.03788 ( 367) hydrogen bonds : angle 4.33124 ( 1050) link_BETA1-4 : bond 0.00084 ( 1) link_BETA1-4 : angle 1.02104 ( 3) link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 1.16541 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7594 (mt0) cc_final: 0.7247 (mm110) REVERT: A 359 GLU cc_start: 0.8345 (mp0) cc_final: 0.8099 (mp0) REVERT: A 366 LYS cc_start: 0.9293 (mmmt) cc_final: 0.9035 (mmmt) REVERT: A 420 PHE cc_start: 0.8494 (m-80) cc_final: 0.8208 (m-80) REVERT: A 430 PHE cc_start: 0.8792 (t80) cc_final: 0.8378 (t80) REVERT: A 434 PHE cc_start: 0.7949 (m-80) cc_final: 0.7557 (m-80) REVERT: C 56 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7535 (p) REVERT: C 66 ILE cc_start: 0.6979 (mt) cc_final: 0.6724 (mp) REVERT: C 90 CYS cc_start: 0.7700 (m) cc_final: 0.7257 (m) REVERT: C 148 PHE cc_start: 0.8452 (m-80) cc_final: 0.8069 (m-80) REVERT: C 214 GLU cc_start: 0.7372 (tp30) cc_final: 0.6764 (tm-30) REVERT: H 10 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8084 (mp0) REVERT: L 17 ASP cc_start: 0.8272 (t0) cc_final: 0.7905 (t0) REVERT: L 105 GLU cc_start: 0.7958 (pm20) cc_final: 0.7372 (pm20) outliers start: 21 outliers final: 17 residues processed: 127 average time/residue: 0.0867 time to fit residues: 14.4994 Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.118465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082168 restraints weight = 16988.444| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.11 r_work: 0.3080 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7847 Z= 0.130 Angle : 0.667 8.246 10718 Z= 0.332 Chirality : 0.042 0.138 1238 Planarity : 0.004 0.057 1325 Dihedral : 5.948 54.786 1269 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.03 % Allowed : 17.58 % Favored : 80.38 % 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: 0.43 (0.28), residues: 940 helix: 0.98 (0.27), residues: 388 sheet: 0.31 (0.40), residues: 170 loop : -0.33 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 103 TYR 0.032 0.001 TYR H 99 PHE 0.017 0.001 PHE A 430 TRP 0.034 0.001 TRP C 145 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7842) covalent geometry : angle 0.66707 (10706) SS BOND : bond 0.00463 ( 3) SS BOND : angle 0.63676 ( 6) hydrogen bonds : bond 0.03518 ( 367) hydrogen bonds : angle 4.19378 ( 1050) link_BETA1-4 : bond 0.00170 ( 1) link_BETA1-4 : angle 1.09997 ( 3) link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 0.89821 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.31 seconds wall clock time: 35 minutes 34.67 seconds (2134.67 seconds total)