Starting phenix.real_space_refine on Mon Sep 14 09:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvu_32148/09_2026/7vvu_32148.map" } resolution = 3.4 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 Anisotropic ADP refinement not supported. Converting 13019 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 362 5.49 5 S 36 5.16 5 C 11082 2.51 5 N 3536 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19374 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 923 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2294 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "S" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "U" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2286 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain: "W" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3666 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Chain: "I" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3695 Classifications: {'DNA': 179} Link IDs: {'rna3p': 178} Chain: "X" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.80, per 1000 atoms: 0.20 Number of scatterers: 19374 At special positions: 0 Unit cell: (123.405, 169.952, 182.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 362 15.00 O 4358 8.00 N 3536 7.00 C 11082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 520.6 milliseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 69.0% alpha, 4.6% beta 164 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'Y' and resid 1 through 45 removed outlier: 3.771A pdb=" N LEU Y 5 " --> pdb=" O MET Y 1 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 16 removed outlier: 4.455A pdb=" N ASN V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 57 removed outlier: 3.905A pdb=" N LYS V 45 " --> pdb=" O LYS V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 113 Processing helix chain 'T' and resid 132 through 137 Processing helix chain 'T' and resid 154 through 158 removed outlier: 3.576A pdb=" N CYS T 158 " --> pdb=" O GLU T 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 176 Processing helix chain 'T' and resid 185 through 204 Processing helix chain 'T' and resid 206 through 214 Proline residue: T 211 - end of helix Processing helix chain 'T' and resid 216 through 227 Proline residue: T 222 - end of helix Processing helix chain 'T' and resid 228 through 230 No H-bonds generated for 'chain 'T' and resid 228 through 230' Processing helix chain 'T' and resid 231 through 242 Processing helix chain 'T' and resid 255 through 260 removed outlier: 3.692A pdb=" N ASN T 260 " --> pdb=" O SER T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 263 through 286 removed outlier: 6.468A pdb=" N SER T 273 " --> pdb=" O GLU T 269 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS T 274 " --> pdb=" O LYS T 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 317 removed outlier: 3.970A pdb=" N GLU T 316 " --> pdb=" O ARG T 313 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 383 removed outlier: 3.600A pdb=" N LEU T 334 " --> pdb=" O ASN T 330 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA T 336 " --> pdb=" O GLN T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 388 through 392 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 removed outlier: 4.027A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'Q' and resid 24 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.842A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.613A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 36 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.519A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'U' and resid 37 through 49 Processing helix chain 'U' and resid 55 through 84 Processing helix chain 'U' and resid 90 through 102 Processing helix chain 'U' and resid 103 through 123 removed outlier: 3.636A pdb=" N ALA U 107 " --> pdb=" O PRO U 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.554A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 19 through 23 removed outlier: 4.243A pdb=" N LEU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.895A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.525A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 26 through 36 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.519A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.531A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 191 removed outlier: 3.535A pdb=" N THR P 190 " --> pdb=" O PRO P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 218 Processing helix chain 'P' and resid 244 through 257 removed outlier: 3.867A pdb=" N LEU P 257 " --> pdb=" O LEU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 309 through 312 Processing helix chain 'P' and resid 315 through 331 Processing helix chain 'P' and resid 342 through 365 Processing helix chain 'P' and resid 369 through 378 Processing helix chain 'P' and resid 380 through 391 Processing helix chain 'P' and resid 406 through 420 removed outlier: 3.513A pdb=" N LEU P 410 " --> pdb=" O ASN P 406 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS P 420 " --> pdb=" O LEU P 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 425 through 429 Processing sheet with id=AA1, first strand: chain 'T' and resid 128 through 129 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.706A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'Q' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.384A pdb=" N ARG S 42 " --> pdb=" O ILE U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'S' and resid 100 through 102 removed outlier: 6.875A pdb=" N THR S 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.944A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.270A pdb=" N ARG N 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'P' and resid 226 through 230 removed outlier: 6.150A pdb=" N GLU P 227 " --> pdb=" O GLU P 238 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU P 238 " --> pdb=" O GLU P 227 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU P 272 " --> pdb=" O SER P 291 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER P 291 " --> pdb=" O LEU P 272 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR P 274 " --> pdb=" O TYR P 289 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR P 289 " --> pdb=" O TYR P 274 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET P 276 " --> pdb=" O VAL P 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 300 through 302 removed outlier: 5.754A pdb=" N SER P 336 " --> pdb=" O TYR P 300 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL P 302 " --> pdb=" O SER P 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'P' and resid 394 through 396 765 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.48 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: 4541 1.33 - 1.45: 5834 1.45 - 1.57: 9321 1.57 - 1.69: 721 1.69 - 1.81: 59 Bond restraints: 20476 Sorted by residual: bond pdb=" O3B CMC B 501 " pdb=" P3B CMC B 501 " ideal model delta sigma weight residual 1.728 1.613 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C3' DC W 109 " pdb=" C2' DC W 109 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.96e+01 bond pdb=" C3' DT I 128 " pdb=" C2' DT I 128 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.89e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.74e+01 bond pdb=" C3' DG I 37 " pdb=" C2' DG I 37 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.60e+01 ... (remaining 20471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 27495 1.64 - 3.28: 1515 3.28 - 4.93: 154 4.93 - 6.57: 16 6.57 - 8.21: 3 Bond angle restraints: 29183 Sorted by residual: angle pdb=" O4' DG I 78 " pdb=" C4' DG I 78 " pdb=" C3' DG I 78 " ideal model delta sigma weight residual 106.00 102.04 3.96 6.00e-01 2.78e+00 4.36e+01 angle pdb=" O4' DG I 52 " pdb=" C1' DG I 52 " pdb=" N9 DG I 52 " ideal model delta sigma weight residual 108.00 111.65 -3.65 7.00e-01 2.04e+00 2.72e+01 angle pdb=" O4' DG I 38 " pdb=" C4' DG I 38 " pdb=" C3' DG I 38 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" O4' DC W 125 " pdb=" C1' DC W 125 " pdb=" N1 DC W 125 " ideal model delta sigma weight residual 108.00 111.41 -3.41 7.00e-01 2.04e+00 2.38e+01 angle pdb=" O4' DG W 121 " pdb=" C1' DG W 121 " pdb=" N9 DG W 121 " ideal model delta sigma weight residual 108.00 104.59 3.41 7.00e-01 2.04e+00 2.37e+01 ... (remaining 29178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 9559 31.89 - 63.77: 1834 63.77 - 95.66: 52 95.66 - 127.54: 4 127.54 - 159.43: 6 Dihedral angle restraints: 11455 sinusoidal: 7143 harmonic: 4312 Sorted by residual: dihedral pdb=" CAP CMC B 501 " pdb=" CBP CMC B 501 " pdb=" CCP CMC B 501 " pdb=" O6A CMC B 501 " ideal model delta sinusoidal sigma weight residual 70.77 -62.95 133.72 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CDP CMC B 501 " pdb=" CBP CMC B 501 " pdb=" CCP CMC B 501 " pdb=" O6A CMC B 501 " ideal model delta sinusoidal sigma weight residual 191.32 57.99 133.33 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CEP CMC B 501 " pdb=" CBP CMC B 501 " pdb=" CCP CMC B 501 " pdb=" O6A CMC B 501 " ideal model delta sinusoidal sigma weight residual 308.64 176.73 131.91 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 11452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2315 0.052 - 0.104: 724 0.104 - 0.156: 200 0.156 - 0.208: 20 0.208 - 0.259: 2 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C4' DG W 16 " pdb=" C5' DG W 16 " pdb=" O4' DG W 16 " pdb=" C3' DG W 16 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' DG I 94 " pdb=" C4' DG I 94 " pdb=" O3' DG I 94 " pdb=" C2' DG I 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1' DG I 53 " pdb=" O4' DG I 53 " pdb=" C2' DG I 53 " pdb=" N9 DG I 53 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3258 not shown) Planarity restraints: 2458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC B 501 " -0.118 2.00e-02 2.50e+03 9.77e-02 1.19e+02 pdb=" C9P CMC B 501 " 0.029 2.00e-02 2.50e+03 pdb=" CAP CMC B 501 " -0.087 2.00e-02 2.50e+03 pdb=" N8P CMC B 501 " 0.159 2.00e-02 2.50e+03 pdb=" O9P CMC B 501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 268 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE T 268 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE T 268 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU T 269 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 154 " 0.019 2.00e-02 2.50e+03 1.87e-02 7.86e+00 pdb=" N1 DC I 154 " -0.045 2.00e-02 2.50e+03 pdb=" C2 DC I 154 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC I 154 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 154 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 154 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 154 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 154 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I 154 " 0.008 2.00e-02 2.50e+03 ... (remaining 2455 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2526 2.75 - 3.29: 18458 3.29 - 3.83: 37503 3.83 - 4.36: 43461 4.36 - 4.90: 64493 Nonbonded interactions: 166441 Sorted by model distance: nonbonded pdb=" OH TYR P 233 " pdb=" OH TYR P 316 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR T 147 " pdb=" O ARG P 428 " model vdw 2.218 3.040 nonbonded pdb=" N PHE T 141 " pdb=" O GLU P 281 " model vdw 2.224 3.120 nonbonded pdb=" OD2 ASP U 68 " pdb=" OH TYR B 98 " model vdw 2.254 3.040 nonbonded pdb=" NH2 ARG S 20 " pdb=" OP1 DG I 32 " model vdw 2.266 3.120 ... (remaining 166436 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 'O' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'Q' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'S' } 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 20477 Z= 0.541 Angle : 0.789 8.209 29183 Z= 0.654 Chirality : 0.054 0.259 3261 Planarity : 0.005 0.098 2458 Dihedral : 24.946 159.430 8661 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.31 % Allowed : 3.24 % Favored : 96.46 % 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: 1.82 (0.22), residues: 1440 helix: 2.20 (0.16), residues: 938 sheet: -0.51 (0.82), residues: 39 loop : -0.75 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 395 TYR 0.017 0.001 TYR P 265 PHE 0.010 0.001 PHE U 70 TRP 0.010 0.002 TRP P 247 HIS 0.006 0.001 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.54 (20476) covalent geometry : angle 0.78896 / 0.65 (29183) hydrogen bonds : bond 0.11246 / 7.49 ( 1188) hydrogen bonds : angle 4.32479 / 3.16 ( 3066) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.605 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: symmetry clash REVERT: Y 27 ASP cc_start: 0.9386 (m-30) cc_final: 0.9099 (m-30) REVERT: V 1 MET cc_start: 0.5044 (mmt) cc_final: 0.4047 (ppp) REVERT: V 14 VAL cc_start: 0.8930 (p) cc_final: 0.8730 (m) REVERT: T 240 HIS cc_start: 0.9370 (t70) cc_final: 0.9086 (m90) REVERT: T 319 HIS cc_start: 0.6083 (p-80) cc_final: 0.5227 (t70) REVERT: O 120 MET cc_start: 0.8674 (mtp) cc_final: 0.8183 (mtt) REVERT: Q 49 LEU cc_start: 0.9824 (mt) cc_final: 0.9194 (mt) REVERT: Q 88 TYR cc_start: 0.9037 (m-10) cc_final: 0.8714 (m-80) REVERT: S 110 ASN cc_start: 0.8589 (t0) cc_final: 0.7962 (t0) REVERT: A 90 MET cc_start: 0.9347 (mmm) cc_final: 0.8958 (mmm) REVERT: A 125 GLN cc_start: 0.9342 (mt0) cc_final: 0.9043 (mp10) REVERT: B 20 LYS cc_start: 0.3922 (OUTLIER) cc_final: 0.2833 (tppt) REVERT: B 53 GLU cc_start: 0.8988 (tp30) cc_final: 0.8681 (tp30) REVERT: B 84 MET cc_start: 0.8972 (mmm) cc_final: 0.8300 (mmm) REVERT: N 56 GLU cc_start: 0.9270 (tt0) cc_final: 0.8776 (tt0) REVERT: N 72 ASP cc_start: 0.8617 (m-30) cc_final: 0.8397 (m-30) REVERT: D 59 MET cc_start: 0.9355 (tpp) cc_final: 0.9017 (tpt) REVERT: P 252 CYS cc_start: 0.9507 (m) cc_final: 0.9169 (m) REVERT: P 254 LEU cc_start: 0.9777 (tp) cc_final: 0.9551 (mt) outliers start: 4 outliers final: 0 residues processed: 234 average time/residue: 0.1745 time to fit residues: 58.6605 Evaluate side-chains 129 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 48 GLN A 93 GLN P 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.082666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046996 restraints weight = 126933.607| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.23 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20477 Z= 0.155 Angle : 0.665 10.801 29183 Z= 0.379 Chirality : 0.044 0.330 3261 Planarity : 0.004 0.045 2458 Dihedral : 29.672 165.671 5596 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.23 % Allowed : 7.86 % Favored : 90.91 % 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: 2.38 (0.22), residues: 1440 helix: 2.64 (0.16), residues: 940 sheet: 0.59 (0.94), residues: 29 loop : -0.61 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 22 TYR 0.017 0.001 TYR A 99 PHE 0.021 0.002 PHE V 21 TRP 0.011 0.002 TRP P 353 HIS 0.007 0.001 HIS O 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (20476) covalent geometry : angle 0.66455 / 0.38 (29183) hydrogen bonds : bond 0.05204 / 3.36 ( 1188) hydrogen bonds : angle 3.76272 / 2.69 ( 3066) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.614 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: symmetry clash REVERT: V 1 MET cc_start: 0.5474 (mmt) cc_final: 0.4327 (ppp) REVERT: T 240 HIS cc_start: 0.9385 (t70) cc_final: 0.9122 (m90) REVERT: T 319 HIS cc_start: 0.5918 (p-80) cc_final: 0.4960 (t70) REVERT: Q 88 TYR cc_start: 0.8866 (m-10) cc_final: 0.8656 (m-80) REVERT: S 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8294 (t0) REVERT: A 90 MET cc_start: 0.9112 (mmm) cc_final: 0.8863 (mmm) REVERT: A 125 GLN cc_start: 0.9111 (mt0) cc_final: 0.8853 (mp10) REVERT: B 63 GLU cc_start: 0.8681 (tp30) cc_final: 0.8373 (tp30) REVERT: B 93 GLN cc_start: 0.8314 (mp10) cc_final: 0.8083 (mp10) REVERT: N 56 GLU cc_start: 0.8956 (tt0) cc_final: 0.8526 (tt0) REVERT: N 90 ASP cc_start: 0.8520 (t0) cc_final: 0.7850 (t0) REVERT: D 76 GLU cc_start: 0.8890 (tp30) cc_final: 0.8346 (mm-30) REVERT: D 108 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9143 (mmmm) REVERT: P 252 CYS cc_start: 0.9329 (m) cc_final: 0.9093 (m) REVERT: P 257 LEU cc_start: 0.9267 (tp) cc_final: 0.9028 (tp) REVERT: P 276 MET cc_start: 0.9041 (tmm) cc_final: 0.8653 (tmm) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.1445 time to fit residues: 35.6571 Evaluate side-chains 138 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain T residue 198 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 31 ASN V 16 ASN B 18 HIS B 25 ASN D 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.080599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046731 restraints weight = 123361.732| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.00 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20477 Z= 0.293 Angle : 0.750 10.313 29183 Z= 0.410 Chirality : 0.045 0.275 3261 Planarity : 0.005 0.043 2458 Dihedral : 29.998 174.512 5592 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 8.55 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.22), residues: 1440 helix: 2.52 (0.16), residues: 951 sheet: 0.14 (1.01), residues: 27 loop : -0.70 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 22 TYR 0.036 0.002 TYR P 349 PHE 0.034 0.002 PHE V 21 TRP 0.050 0.003 TRP P 353 HIS 0.009 0.002 HIS Q 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.29 (20476) covalent geometry : angle 0.74964 / 0.41 (29183) hydrogen bonds : bond 0.07485 / 4.94 ( 1188) hydrogen bonds : angle 4.03571 / 2.90 ( 3066) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5173 (mmt) cc_final: 0.4448 (ppp) REVERT: T 319 HIS cc_start: 0.5994 (p-80) cc_final: 0.4957 (t70) REVERT: Q 88 TYR cc_start: 0.8932 (m-10) cc_final: 0.8656 (m-80) REVERT: A 90 MET cc_start: 0.9185 (mmm) cc_final: 0.8921 (mmm) REVERT: A 105 GLU cc_start: 0.8814 (tp30) cc_final: 0.8482 (tp30) REVERT: A 125 GLN cc_start: 0.9134 (mt0) cc_final: 0.8873 (mp10) REVERT: B 84 MET cc_start: 0.8595 (mmm) cc_final: 0.7864 (mmm) REVERT: B 93 GLN cc_start: 0.8660 (mp10) cc_final: 0.8315 (mp10) REVERT: N 56 GLU cc_start: 0.8975 (tt0) cc_final: 0.8710 (tt0) REVERT: D 33 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7589 (mtt180) REVERT: D 76 GLU cc_start: 0.8985 (tp30) cc_final: 0.8458 (mm-30) REVERT: P 252 CYS cc_start: 0.9540 (m) cc_final: 0.9325 (m) REVERT: P 257 LEU cc_start: 0.9348 (tp) cc_final: 0.9121 (tp) REVERT: P 276 MET cc_start: 0.9015 (tmm) cc_final: 0.8604 (tmm) REVERT: P 353 TRP cc_start: 0.9145 (m-10) cc_final: 0.8915 (m-90) REVERT: P 379 MET cc_start: 0.8723 (tpp) cc_final: 0.8349 (tpp) outliers start: 27 outliers final: 18 residues processed: 145 average time/residue: 0.1351 time to fit residues: 31.5617 Evaluate side-chains 142 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain T residue 395 LYS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 334 VAL Chi-restraints excluded: chain P residue 371 ASP Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 60.0000 chunk 47 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046009 restraints weight = 128749.101| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.23 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 20477 Z= 0.377 Angle : 0.840 13.698 29183 Z= 0.453 Chirality : 0.049 0.304 3261 Planarity : 0.006 0.048 2458 Dihedral : 30.373 169.695 5592 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.00 % Allowed : 10.63 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.21), residues: 1440 helix: 1.85 (0.16), residues: 957 sheet: -0.06 (1.02), residues: 25 loop : -0.82 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.023 0.002 TYR P 349 PHE 0.050 0.003 PHE V 21 TRP 0.028 0.003 TRP P 353 HIS 0.012 0.003 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.38 (20476) covalent geometry : angle 0.83957 / 0.45 (29183) hydrogen bonds : bond 0.07368 / 4.83 ( 1188) hydrogen bonds : angle 4.41431 / 3.18 ( 3066) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5618 (mmt) cc_final: 0.5268 (ppp) REVERT: T 319 HIS cc_start: 0.6219 (p-80) cc_final: 0.5042 (t70) REVERT: S 110 ASN cc_start: 0.8385 (m110) cc_final: 0.7884 (p0) REVERT: U 59 MET cc_start: 0.9454 (tpp) cc_final: 0.9208 (tpp) REVERT: A 90 MET cc_start: 0.9235 (mmm) cc_final: 0.8970 (mmm) REVERT: A 125 GLN cc_start: 0.9076 (mt0) cc_final: 0.8833 (mp10) REVERT: B 35 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8693 (mtp-110) REVERT: B 53 GLU cc_start: 0.9117 (tp30) cc_final: 0.8908 (tp30) REVERT: B 74 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8374 (pp20) REVERT: B 84 MET cc_start: 0.8640 (mmm) cc_final: 0.7883 (mmm) REVERT: N 90 ASP cc_start: 0.9062 (t0) cc_final: 0.8538 (t0) REVERT: D 33 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7684 (mtt180) REVERT: D 76 GLU cc_start: 0.9004 (tp30) cc_final: 0.8501 (mm-30) REVERT: P 252 CYS cc_start: 0.9670 (m) cc_final: 0.9421 (m) REVERT: P 276 MET cc_start: 0.9133 (tmm) cc_final: 0.8774 (tmm) REVERT: P 379 MET cc_start: 0.8571 (tpp) cc_final: 0.8140 (tpp) outliers start: 26 outliers final: 15 residues processed: 136 average time/residue: 0.1414 time to fit residues: 30.1942 Evaluate side-chains 124 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain T residue 395 LYS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 370 ILE Chi-restraints excluded: chain P residue 371 ASP Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 150 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 120 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 46 HIS T 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.079483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042979 restraints weight = 128519.310| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.28 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20477 Z= 0.261 Angle : 0.714 12.103 29183 Z= 0.396 Chirality : 0.045 0.280 3261 Planarity : 0.005 0.077 2458 Dihedral : 30.186 171.678 5592 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.77 % Allowed : 11.48 % Favored : 86.75 % 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: 1.80 (0.22), residues: 1440 helix: 2.14 (0.16), residues: 957 sheet: -0.27 (1.00), residues: 25 loop : -0.79 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 92 TYR 0.015 0.002 TYR P 265 PHE 0.061 0.002 PHE V 21 TRP 0.012 0.002 TRP P 353 HIS 0.009 0.002 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.26 (20476) covalent geometry : angle 0.71373 / 0.40 (29183) hydrogen bonds : bond 0.06349 / 4.19 ( 1188) hydrogen bonds : angle 4.09838 / 2.94 ( 3066) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 319 HIS cc_start: 0.6248 (p-80) cc_final: 0.5035 (t70) REVERT: S 110 ASN cc_start: 0.8340 (m110) cc_final: 0.7900 (p0) REVERT: A 90 MET cc_start: 0.9157 (mmm) cc_final: 0.8930 (mmm) REVERT: A 125 GLN cc_start: 0.9072 (mt0) cc_final: 0.8808 (mp10) REVERT: B 35 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8660 (mtp-110) REVERT: B 53 GLU cc_start: 0.9012 (tp30) cc_final: 0.8774 (tp30) REVERT: B 93 GLN cc_start: 0.8910 (mp10) cc_final: 0.8373 (mp10) REVERT: D 33 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7694 (mtt180) REVERT: D 76 GLU cc_start: 0.8982 (tp30) cc_final: 0.8416 (mm-30) REVERT: P 252 CYS cc_start: 0.9625 (m) cc_final: 0.9339 (m) REVERT: P 276 MET cc_start: 0.9042 (tmm) cc_final: 0.8670 (tmm) REVERT: P 314 MET cc_start: 0.8797 (mtt) cc_final: 0.8564 (ptp) REVERT: P 353 TRP cc_start: 0.9123 (m-10) cc_final: 0.8837 (m-90) REVERT: P 379 MET cc_start: 0.8739 (tpp) cc_final: 0.8317 (tpp) outliers start: 23 outliers final: 15 residues processed: 135 average time/residue: 0.1423 time to fit residues: 30.3185 Evaluate side-chains 130 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain Y residue 46 HIS Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain V residue 21 PHE Chi-restraints excluded: chain T residue 395 LYS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 50.0000 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 175 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 141 optimal weight: 90.0000 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.043734 restraints weight = 128097.229| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.11 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20477 Z= 0.235 Angle : 0.690 11.471 29183 Z= 0.384 Chirality : 0.044 0.281 3261 Planarity : 0.004 0.046 2458 Dihedral : 30.122 172.323 5592 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 11.71 % Favored : 86.36 % 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: 1.98 (0.22), residues: 1440 helix: 2.31 (0.16), residues: 957 sheet: -0.40 (0.99), residues: 25 loop : -0.79 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.015 0.002 TYR P 265 PHE 0.057 0.002 PHE V 21 TRP 0.009 0.002 TRP P 353 HIS 0.022 0.002 HIS Y 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (20476) covalent geometry : angle 0.68962 / 0.38 (29183) hydrogen bonds : bond 0.05820 / 3.81 ( 1188) hydrogen bonds : angle 3.94855 / 2.83 ( 3066) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 176 VAL cc_start: 0.3195 (OUTLIER) cc_final: 0.2955 (t) REVERT: T 319 HIS cc_start: 0.6345 (OUTLIER) cc_final: 0.5089 (t70) REVERT: S 110 ASN cc_start: 0.8318 (m110) cc_final: 0.7896 (p0) REVERT: A 90 MET cc_start: 0.9142 (mmm) cc_final: 0.8893 (mmm) REVERT: A 125 GLN cc_start: 0.9086 (mt0) cc_final: 0.8799 (mp10) REVERT: B 35 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8661 (mtp-110) REVERT: B 53 GLU cc_start: 0.9023 (tp30) cc_final: 0.8758 (tp30) REVERT: B 93 GLN cc_start: 0.8900 (mp10) cc_final: 0.8362 (mp10) REVERT: D 76 GLU cc_start: 0.8957 (tp30) cc_final: 0.8376 (mm-30) REVERT: P 252 CYS cc_start: 0.9638 (m) cc_final: 0.9347 (m) REVERT: P 276 MET cc_start: 0.9009 (tmm) cc_final: 0.8653 (tmm) REVERT: P 314 MET cc_start: 0.8774 (mtt) cc_final: 0.8542 (ptp) REVERT: P 353 TRP cc_start: 0.9134 (m-10) cc_final: 0.8813 (m-90) REVERT: P 379 MET cc_start: 0.8699 (tpp) cc_final: 0.8271 (tpp) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.1369 time to fit residues: 28.6299 Evaluate side-chains 132 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain V residue 21 PHE Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.081137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048145 restraints weight = 125817.554| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.10 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20477 Z= 0.142 Angle : 0.620 10.093 29183 Z= 0.355 Chirality : 0.042 0.290 3261 Planarity : 0.004 0.046 2458 Dihedral : 29.928 173.680 5592 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.46 % Allowed : 12.56 % Favored : 85.98 % 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: 2.26 (0.22), residues: 1440 helix: 2.50 (0.16), residues: 965 sheet: -0.31 (0.97), residues: 25 loop : -0.68 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 22 TYR 0.014 0.001 TYR P 265 PHE 0.056 0.002 PHE V 21 TRP 0.014 0.001 TRP P 353 HIS 0.009 0.001 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (20476) covalent geometry : angle 0.61974 / 0.36 (29183) hydrogen bonds : bond 0.04425 / 2.89 ( 1188) hydrogen bonds : angle 3.61858 / 2.57 ( 3066) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 176 VAL cc_start: 0.2997 (OUTLIER) cc_final: 0.2756 (t) REVERT: T 319 HIS cc_start: 0.6221 (OUTLIER) cc_final: 0.5054 (t70) REVERT: A 90 MET cc_start: 0.9230 (mmm) cc_final: 0.8969 (mmm) REVERT: A 125 GLN cc_start: 0.9080 (mt0) cc_final: 0.8756 (mp10) REVERT: B 74 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8290 (pp20) REVERT: B 93 GLN cc_start: 0.8873 (mp10) cc_final: 0.8647 (mp10) REVERT: D 76 GLU cc_start: 0.8964 (tp30) cc_final: 0.8373 (mm-30) REVERT: P 252 CYS cc_start: 0.9622 (m) cc_final: 0.9368 (m) REVERT: P 276 MET cc_start: 0.9210 (tmm) cc_final: 0.8812 (tmm) REVERT: P 314 MET cc_start: 0.9030 (mtt) cc_final: 0.8666 (ptp) REVERT: P 353 TRP cc_start: 0.9316 (m-10) cc_final: 0.8917 (m-90) REVERT: P 379 MET cc_start: 0.8803 (tpp) cc_final: 0.8390 (tpp) outliers start: 19 outliers final: 15 residues processed: 137 average time/residue: 0.1405 time to fit residues: 30.6070 Evaluate side-chains 139 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 240 HIS Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.080634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048053 restraints weight = 125469.984| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.99 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20477 Z= 0.173 Angle : 0.630 9.694 29183 Z= 0.357 Chirality : 0.041 0.299 3261 Planarity : 0.004 0.045 2458 Dihedral : 29.875 175.632 5592 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.54 % Allowed : 12.40 % Favored : 86.06 % 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: 2.34 (0.22), residues: 1440 helix: 2.56 (0.16), residues: 965 sheet: -0.31 (0.97), residues: 25 loop : -0.66 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 29 TYR 0.014 0.001 TYR P 265 PHE 0.063 0.001 PHE V 21 TRP 0.009 0.001 TRP P 353 HIS 0.014 0.001 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (20476) covalent geometry : angle 0.62995 / 0.36 (29183) hydrogen bonds : bond 0.04851 / 3.16 ( 1188) hydrogen bonds : angle 3.63286 / 2.60 ( 3066) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 176 VAL cc_start: 0.2712 (OUTLIER) cc_final: 0.2455 (t) REVERT: T 319 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5111 (t70) REVERT: S 110 ASN cc_start: 0.8252 (m110) cc_final: 0.7821 (p0) REVERT: A 90 MET cc_start: 0.9187 (mmm) cc_final: 0.8937 (mmm) REVERT: A 125 GLN cc_start: 0.9071 (mt0) cc_final: 0.8786 (mp10) REVERT: B 93 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: D 76 GLU cc_start: 0.8984 (tp30) cc_final: 0.8364 (mm-30) REVERT: P 252 CYS cc_start: 0.9624 (m) cc_final: 0.9369 (m) REVERT: P 276 MET cc_start: 0.9187 (tmm) cc_final: 0.8837 (tmm) REVERT: P 353 TRP cc_start: 0.9292 (m-10) cc_final: 0.8904 (m-90) REVERT: P 379 MET cc_start: 0.8811 (tpp) cc_final: 0.8396 (tpp) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.1339 time to fit residues: 27.9038 Evaluate side-chains 137 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain V residue 21 PHE Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.080689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.047875 restraints weight = 125131.879| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.04 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20477 Z= 0.152 Angle : 0.616 9.363 29183 Z= 0.353 Chirality : 0.041 0.321 3261 Planarity : 0.004 0.045 2458 Dihedral : 29.738 178.643 5592 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.31 % Allowed : 13.02 % Favored : 85.67 % 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: 2.43 (0.22), residues: 1440 helix: 2.62 (0.16), residues: 966 sheet: -0.29 (0.95), residues: 25 loop : -0.60 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.021 0.001 TYR P 316 PHE 0.062 0.001 PHE V 21 TRP 0.010 0.001 TRP P 353 HIS 0.011 0.001 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (20476) covalent geometry : angle 0.61603 / 0.35 (29183) hydrogen bonds : bond 0.04437 / 2.90 ( 1188) hydrogen bonds : angle 3.53101 / 2.51 ( 3066) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 176 VAL cc_start: 0.2308 (OUTLIER) cc_final: 0.2036 (t) REVERT: T 319 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5121 (t70) REVERT: S 110 ASN cc_start: 0.8345 (m110) cc_final: 0.7915 (p0) REVERT: A 90 MET cc_start: 0.9153 (mmm) cc_final: 0.8934 (mmm) REVERT: A 125 GLN cc_start: 0.9044 (mt0) cc_final: 0.8730 (mp10) REVERT: B 74 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8239 (pp20) REVERT: B 84 MET cc_start: 0.8325 (tpp) cc_final: 0.8078 (mmm) REVERT: B 93 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: D 33 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6477 (mmt-90) REVERT: D 76 GLU cc_start: 0.8959 (tp30) cc_final: 0.8382 (mm-30) REVERT: P 252 CYS cc_start: 0.9617 (m) cc_final: 0.9355 (m) REVERT: P 276 MET cc_start: 0.9162 (tmm) cc_final: 0.8782 (tmm) REVERT: P 353 TRP cc_start: 0.9267 (m-10) cc_final: 0.8894 (m-90) REVERT: P 379 MET cc_start: 0.8811 (tpp) cc_final: 0.8451 (tpp) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.1313 time to fit residues: 27.5938 Evaluate side-chains 139 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain V residue 21 PHE Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 141 optimal weight: 70.0000 chunk 154 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 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 = 0.3951 r_free = 0.3951 target = 0.080621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.044529 restraints weight = 126299.873| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.12 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20477 Z= 0.151 Angle : 0.622 9.235 29183 Z= 0.353 Chirality : 0.041 0.335 3261 Planarity : 0.004 0.044 2458 Dihedral : 29.684 179.167 5592 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.16 % Allowed : 13.25 % Favored : 85.59 % 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: 2.49 (0.22), residues: 1440 helix: 2.67 (0.16), residues: 966 sheet: -0.28 (0.95), residues: 25 loop : -0.56 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.014 0.001 TYR P 265 PHE 0.061 0.001 PHE V 21 TRP 0.008 0.001 TRP P 353 HIS 0.009 0.001 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (20476) covalent geometry : angle 0.62181 / 0.35 (29183) hydrogen bonds : bond 0.04531 / 2.96 ( 1188) hydrogen bonds : angle 3.51429 / 2.50 ( 3066) Misc. bond : bond 0.00006 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 176 VAL cc_start: 0.2407 (OUTLIER) cc_final: 0.2146 (t) REVERT: T 319 HIS cc_start: 0.6319 (p-80) cc_final: 0.5191 (t70) REVERT: S 110 ASN cc_start: 0.8330 (m110) cc_final: 0.7957 (p0) REVERT: A 125 GLN cc_start: 0.9083 (mt0) cc_final: 0.8747 (mp10) REVERT: B 74 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8286 (pp20) REVERT: D 33 ARG cc_start: 0.7717 (mtt180) cc_final: 0.6207 (mmt180) REVERT: D 76 GLU cc_start: 0.8992 (tp30) cc_final: 0.8357 (mm-30) REVERT: P 252 CYS cc_start: 0.9552 (m) cc_final: 0.9255 (m) REVERT: P 276 MET cc_start: 0.8941 (tmm) cc_final: 0.8617 (tmm) REVERT: P 353 TRP cc_start: 0.9100 (m-10) cc_final: 0.8787 (m-90) REVERT: P 379 MET cc_start: 0.8756 (tpp) cc_final: 0.8416 (tpp) outliers start: 15 outliers final: 12 residues processed: 132 average time/residue: 0.1366 time to fit residues: 29.1456 Evaluate side-chains 136 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain V residue 21 PHE Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain X residue 59 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 174 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 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 = 0.3965 r_free = 0.3965 target = 0.081133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.046681 restraints weight = 126309.756| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.23 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20477 Z= 0.129 Angle : 0.618 16.317 29183 Z= 0.351 Chirality : 0.041 0.358 3261 Planarity : 0.004 0.043 2458 Dihedral : 29.554 176.029 5592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.08 % Allowed : 13.56 % Favored : 85.36 % 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: 2.55 (0.22), residues: 1440 helix: 2.70 (0.16), residues: 966 sheet: -0.69 (0.92), residues: 27 loop : -0.47 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 313 TYR 0.013 0.001 TYR P 265 PHE 0.060 0.001 PHE V 21 TRP 0.013 0.001 TRP P 353 HIS 0.009 0.001 HIS T 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (20476) covalent geometry : angle 0.61806 / 0.35 (29183) hydrogen bonds : bond 0.04094 / 2.70 ( 1188) hydrogen bonds : angle 3.41212 / 2.42 ( 3066) Misc. bond : bond 0.00017 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5298.84 seconds wall clock time: 91 minutes 13.71 seconds (5473.71 seconds total)