Starting phenix.real_space_refine on Wed Aug 5 17:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.map" model { file = "/net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p0u_17338/08_2026/8p0u_17338.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6853 2.51 5 N 1891 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5015 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4676 Classifications: {'peptide': 587} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 555} Chain breaks: 2 Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 833 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain breaks: 2 Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "V" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.23 Number of scatterers: 10912 At special positions: 0 Unit cell: (101.721, 121.569, 100.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 18 15.00 Mg 1 11.99 O 2086 8.00 N 1891 7.00 C 6853 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=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 421.6 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2486 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 49.9% alpha, 11.4% beta 2 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.970A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.563A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.690A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 280 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.878A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.481A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.578A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.652A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.524A pdb=" N MET A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.974A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 Proline residue: B 44 - end of helix removed outlier: 4.653A pdb=" N TYR B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.603A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 276 through 287 removed outlier: 4.378A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.727A pdb=" N CYS B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.506A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.420A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.717A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.591A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 568 through 572 removed outlier: 4.297A pdb=" N MET B 572 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'C' and resid 57 through 69 removed outlier: 5.175A pdb=" N VAL C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 114 removed outlier: 4.281A pdb=" N ASP C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 removed outlier: 4.681A pdb=" N ALA C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.061A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.256A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.704A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 4.667A pdb=" N THR B 228 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 345 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS B 387 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 73 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 84 through 85 527 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3323 1.33 - 1.45: 1649 1.45 - 1.57: 6079 1.57 - 1.69: 34 1.69 - 1.81: 104 Bond restraints: 11189 Sorted by residual: bond pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.71e+00 bond pdb=" N TYR B 624 " pdb=" CA TYR B 624 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.14e-02 7.69e+03 6.47e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP B 623 " pdb=" CA ASP B 623 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.28e+00 bond pdb=" CA SER B 625 " pdb=" CB SER B 625 " ideal model delta sigma weight residual 1.529 1.506 0.022 1.66e-02 3.63e+03 1.79e+00 ... (remaining 11184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 14479 0.88 - 1.76: 564 1.76 - 2.64: 113 2.64 - 3.52: 62 3.52 - 4.40: 23 Bond angle restraints: 15241 Sorted by residual: angle pdb=" O5' A V 7 " pdb=" C5' A V 7 " pdb=" C4' A V 7 " ideal model delta sigma weight residual 109.40 112.19 -2.79 8.00e-01 1.56e+00 1.22e+01 angle pdb=" C ASN A 524 " pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " ideal model delta sigma weight residual 111.01 115.41 -4.40 1.38e+00 5.25e-01 1.02e+01 angle pdb=" CA SER B 625 " pdb=" C SER B 625 " pdb=" O SER B 625 " ideal model delta sigma weight residual 121.56 118.16 3.40 1.09e+00 8.42e-01 9.73e+00 angle pdb=" O5' C R 31 " pdb=" C5' C R 31 " pdb=" C4' C R 31 " ideal model delta sigma weight residual 109.40 111.86 -2.46 8.00e-01 1.56e+00 9.46e+00 angle pdb=" O5' U V 8 " pdb=" C5' U V 8 " pdb=" C4' U V 8 " ideal model delta sigma weight residual 109.40 111.80 -2.40 8.00e-01 1.56e+00 8.98e+00 ... (remaining 15236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 6045 20.88 - 41.75: 552 41.75 - 62.63: 161 62.63 - 83.51: 35 83.51 - 104.38: 8 Dihedral angle restraints: 6801 sinusoidal: 2968 harmonic: 3833 Sorted by residual: dihedral pdb=" CG ARG B 122 " pdb=" CD ARG B 122 " pdb=" NE ARG B 122 " pdb=" CZ ARG B 122 " ideal model delta sinusoidal sigma weight residual 90.00 41.35 48.65 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " pdb=" OD1 ASP B 348 " ideal model delta sinusoidal sigma weight residual -30.00 -88.53 58.53 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 575 " pdb=" CB ASP B 575 " pdb=" CG ASP B 575 " pdb=" OD1 ASP B 575 " ideal model delta sinusoidal sigma weight residual -30.00 -87.34 57.34 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 6798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1137 0.030 - 0.059: 390 0.059 - 0.089: 83 0.089 - 0.118: 86 0.118 - 0.148: 13 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CA ASN A 524 " pdb=" N ASN A 524 " pdb=" C ASN A 524 " pdb=" CB ASN A 524 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE B 385 " pdb=" N ILE B 385 " pdb=" C ILE B 385 " pdb=" CB ILE B 385 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1706 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 122 " 0.209 9.50e-02 1.11e+02 9.41e-02 5.98e+00 pdb=" NE ARG B 122 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 122 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 122 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 122 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 524 " 0.008 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ASN A 524 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN A 524 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 525 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.008 2.00e-02 2.50e+03 8.34e-03 1.39e+00 pdb=" CG TYR A 39 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 70 2.50 - 3.10: 7831 3.10 - 3.70: 16986 3.70 - 4.30: 25470 4.30 - 4.90: 42315 Nonbonded interactions: 92672 Sorted by model distance: nonbonded pdb=" OD1 ASP B 423 " pdb="MG MG B 801 " model vdw 1.895 2.170 nonbonded pdb=" OG1 THR A 178 " pdb=" OE1 GLU B 170 " model vdw 2.066 3.040 nonbonded pdb=" OG1 THR A 158 " pdb=" OE1 GLU B 100 " model vdw 2.086 3.040 nonbonded pdb=" O ASN A 524 " pdb=" OD1 ASN A 524 " model vdw 2.118 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OP1 G V 2 " model vdw 2.130 3.040 ... (remaining 92667 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: 5.000 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 0.033 11189 Z= 0.114 Angle : 0.469 4.404 15241 Z= 0.265 Chirality : 0.038 0.148 1709 Planarity : 0.003 0.094 1886 Dihedral : 17.808 104.385 4315 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 3.00 % Allowed : 19.18 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1296 helix: 1.99 (0.22), residues: 589 sheet: -0.85 (0.40), residues: 143 loop : -0.78 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 122 TYR 0.020 0.001 TYR A 39 PHE 0.009 0.001 PHE A 144 TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11189) covalent geometry : angle 0.46867 / 0.26 (15241) hydrogen bonds : bond 0.13371 / 8.69 ( 528) hydrogen bonds : angle 5.16197 / 3.70 ( 1432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.448 Fit side-chains REVERT: C 726 ILE cc_start: 0.8134 (mt) cc_final: 0.7766 (tp) REVERT: C 728 SER cc_start: 0.8154 (t) cc_final: 0.7864 (p) outliers start: 35 outliers final: 24 residues processed: 151 average time/residue: 0.6510 time to fit residues: 105.6936 Evaluate side-chains 108 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 114 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 ASN A 524 ASN A 535 GLN A 603 ASN B 129 HIS B 227 ASN B 397 ASN B 453 ASN B 531 HIS B 582 HIS C 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.048896 restraints weight = 37829.791| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.82 r_work: 0.2688 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11189 Z= 0.138 Angle : 0.555 9.058 15241 Z= 0.287 Chirality : 0.040 0.165 1709 Planarity : 0.005 0.049 1886 Dihedral : 11.074 103.339 1718 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 3.85 % Allowed : 21.49 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.67 (0.24), residues: 1296 helix: 1.88 (0.22), residues: 589 sheet: -1.01 (0.39), residues: 143 loop : -0.69 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 151 TYR 0.012 0.001 TYR B 533 PHE 0.010 0.001 PHE B 127 TRP 0.047 0.001 TRP A 13 HIS 0.006 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11189) covalent geometry : angle 0.55510 / 0.29 (15241) hydrogen bonds : bond 0.04064 / 2.68 ( 528) hydrogen bonds : angle 4.46830 / 3.21 ( 1432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.455 Fit side-chains REVERT: A 14 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8698 (pp20) REVERT: A 32 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8673 (ttt90) REVERT: A 171 LEU cc_start: 0.9005 (tp) cc_final: 0.8784 (tp) REVERT: C 91 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8565 (mtmm) REVERT: C 133 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8090 (t0) REVERT: C 137 GLN cc_start: 0.8515 (mp10) cc_final: 0.8028 (mp10) REVERT: C 726 ILE cc_start: 0.8452 (mt) cc_final: 0.8092 (tp) outliers start: 45 outliers final: 10 residues processed: 126 average time/residue: 0.6086 time to fit residues: 83.2386 Evaluate side-chains 91 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 GLN B 429 ASN B 531 HIS C 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.066174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.047816 restraints weight = 37994.627| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.82 r_work: 0.2658 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11189 Z= 0.194 Angle : 0.548 9.458 15241 Z= 0.276 Chirality : 0.040 0.157 1709 Planarity : 0.004 0.045 1886 Dihedral : 10.822 102.705 1701 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 3.08 % Allowed : 21.75 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.69 (0.24), residues: 1296 helix: 1.81 (0.22), residues: 592 sheet: -0.94 (0.39), residues: 143 loop : -0.60 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 122 TYR 0.015 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.049 0.002 TRP A 13 HIS 0.006 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (11189) covalent geometry : angle 0.54775 / 0.28 (15241) hydrogen bonds : bond 0.04104 / 2.74 ( 528) hydrogen bonds : angle 4.36482 / 3.12 ( 1432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9014 (pp20) REVERT: A 32 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8744 (tmt90) REVERT: B 478 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8637 (p0) REVERT: C 91 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8547 (mtmm) REVERT: C 137 GLN cc_start: 0.8492 (mp10) cc_final: 0.8018 (mp10) REVERT: C 148 ARG cc_start: 0.7513 (pmm150) cc_final: 0.7312 (pmm-80) REVERT: C 726 ILE cc_start: 0.8601 (mt) cc_final: 0.8131 (tp) outliers start: 36 outliers final: 13 residues processed: 108 average time/residue: 0.6408 time to fit residues: 75.0093 Evaluate side-chains 95 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 91 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 535 GLN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.040940 restraints weight = 38947.324| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.79 r_work: 0.2639 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11189 Z= 0.215 Angle : 0.554 10.972 15241 Z= 0.276 Chirality : 0.041 0.149 1709 Planarity : 0.004 0.046 1886 Dihedral : 10.749 102.014 1698 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 3.60 % Allowed : 22.09 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.65 (0.24), residues: 1296 helix: 1.70 (0.22), residues: 598 sheet: -0.88 (0.39), residues: 143 loop : -0.58 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.015 0.001 TYR B 533 PHE 0.013 0.001 PHE B 145 TRP 0.015 0.001 TRP A 13 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (11189) covalent geometry : angle 0.55407 / 0.28 (15241) hydrogen bonds : bond 0.04071 / 2.73 ( 528) hydrogen bonds : angle 4.30424 / 3.08 ( 1432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8821 (p) REVERT: C 91 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8540 (mtmm) REVERT: C 726 ILE cc_start: 0.8609 (mt) cc_final: 0.8087 (tp) outliers start: 42 outliers final: 17 residues processed: 115 average time/residue: 0.5748 time to fit residues: 72.0129 Evaluate side-chains 96 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 535 GLN B 227 ASN B 531 HIS C 119 GLN C 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.041744 restraints weight = 38293.466| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.79 r_work: 0.2670 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11189 Z= 0.125 Angle : 0.519 10.188 15241 Z= 0.259 Chirality : 0.039 0.132 1709 Planarity : 0.004 0.043 1886 Dihedral : 10.715 102.683 1697 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 2.57 % Allowed : 23.12 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.75 (0.24), residues: 1296 helix: 1.80 (0.21), residues: 597 sheet: -0.91 (0.39), residues: 143 loop : -0.52 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.011 0.001 TYR B 533 PHE 0.011 0.001 PHE B 145 TRP 0.012 0.001 TRP A 13 HIS 0.008 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (11189) covalent geometry : angle 0.51944 / 0.26 (15241) hydrogen bonds : bond 0.03688 / 2.44 ( 528) hydrogen bonds : angle 4.22332 / 3.03 ( 1432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8807 (tp) REVERT: A 362 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8835 (p) REVERT: C 726 ILE cc_start: 0.8591 (mt) cc_final: 0.8104 (tp) outliers start: 30 outliers final: 16 residues processed: 100 average time/residue: 0.6078 time to fit residues: 66.1085 Evaluate side-chains 96 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047468 restraints weight = 38466.491| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.75 r_work: 0.2669 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11189 Z= 0.180 Angle : 0.537 10.589 15241 Z= 0.266 Chirality : 0.040 0.150 1709 Planarity : 0.004 0.045 1886 Dihedral : 10.690 102.320 1696 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.61 % Rotamer: Outliers : 2.48 % Allowed : 23.37 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.78 (0.24), residues: 1296 helix: 1.78 (0.21), residues: 598 sheet: -0.82 (0.40), residues: 143 loop : -0.46 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 122 TYR 0.014 0.001 TYR B 533 PHE 0.013 0.001 PHE B 145 TRP 0.011 0.001 TRP B 230 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (11189) covalent geometry : angle 0.53692 / 0.27 (15241) hydrogen bonds : bond 0.03826 / 2.55 ( 528) hydrogen bonds : angle 4.21155 / 3.01 ( 1432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 726 ILE cc_start: 0.8612 (mt) cc_final: 0.8106 (tp) outliers start: 29 outliers final: 16 residues processed: 103 average time/residue: 0.5318 time to fit residues: 59.3769 Evaluate side-chains 93 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048281 restraints weight = 38495.089| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.76 r_work: 0.2696 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11189 Z= 0.115 Angle : 0.523 11.708 15241 Z= 0.257 Chirality : 0.039 0.177 1709 Planarity : 0.003 0.042 1886 Dihedral : 10.655 102.897 1696 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.97 % Allowed : 23.72 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.24), residues: 1296 helix: 1.86 (0.21), residues: 598 sheet: -0.79 (0.40), residues: 143 loop : -0.40 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.011 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.010 0.001 TRP B 230 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11189) covalent geometry : angle 0.52271 / 0.26 (15241) hydrogen bonds : bond 0.03528 / 2.35 ( 528) hydrogen bonds : angle 4.14789 / 2.98 ( 1432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8944 (p) REVERT: C 91 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8585 (mtmm) REVERT: C 726 ILE cc_start: 0.8626 (mt) cc_final: 0.8106 (tp) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 0.5384 time to fit residues: 57.1532 Evaluate side-chains 91 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.0060 chunk 7 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 HIS C 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048106 restraints weight = 38309.660| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.75 r_work: 0.2690 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 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 : 0.003 0.032 11189 Z= 0.136 Angle : 0.536 13.225 15241 Z= 0.267 Chirality : 0.039 0.171 1709 Planarity : 0.004 0.042 1886 Dihedral : 10.644 102.705 1696 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.88 % Allowed : 23.97 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.92 (0.24), residues: 1296 helix: 1.86 (0.21), residues: 598 sheet: -0.76 (0.40), residues: 143 loop : -0.35 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.012 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.010 0.001 TRP A 336 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11189) covalent geometry : angle 0.53624 / 0.27 (15241) hydrogen bonds : bond 0.03639 / 2.42 ( 528) hydrogen bonds : angle 4.12320 / 2.96 ( 1432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8954 (p) REVERT: B 140 GLU cc_start: 0.8861 (tp30) cc_final: 0.8589 (tp30) REVERT: C 83 LEU cc_start: 0.9486 (tm) cc_final: 0.9273 (tm) REVERT: C 91 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8627 (mtmm) REVERT: C 726 ILE cc_start: 0.8604 (mt) cc_final: 0.8046 (tp) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.5603 time to fit residues: 59.1485 Evaluate side-chains 93 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 721 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048680 restraints weight = 38250.434| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.72 r_work: 0.2703 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 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 0.027 11189 Z= 0.115 Angle : 0.525 13.794 15241 Z= 0.260 Chirality : 0.039 0.182 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.608 102.785 1696 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.54 % Allowed : 24.49 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.97 (0.24), residues: 1296 helix: 1.90 (0.22), residues: 598 sheet: -0.76 (0.39), residues: 143 loop : -0.31 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 138 TYR 0.011 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.012 0.001 TRP C 144 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (11189) covalent geometry : angle 0.52456 / 0.26 (15241) hydrogen bonds : bond 0.03507 / 2.33 ( 528) hydrogen bonds : angle 4.08949 / 2.94 ( 1432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 140 GLU cc_start: 0.8846 (tp30) cc_final: 0.8574 (tp30) REVERT: C 726 ILE cc_start: 0.8597 (mt) cc_final: 0.8010 (tp) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.5299 time to fit residues: 54.0178 Evaluate side-chains 89 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048737 restraints weight = 38230.768| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.72 r_work: 0.2704 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11189 Z= 0.121 Angle : 0.538 13.705 15241 Z= 0.263 Chirality : 0.039 0.200 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.575 102.505 1696 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.71 % Allowed : 24.23 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1296 helix: 1.89 (0.22), residues: 599 sheet: -0.66 (0.40), residues: 143 loop : -0.28 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.012 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.016 0.001 TRP C 144 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11189) covalent geometry : angle 0.53752 / 0.26 (15241) hydrogen bonds : bond 0.03473 / 2.32 ( 528) hydrogen bonds : angle 4.04610 / 2.91 ( 1432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9025 (p) REVERT: B 140 GLU cc_start: 0.8839 (tp30) cc_final: 0.8561 (tp30) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.5901 time to fit residues: 61.2682 Evaluate side-chains 92 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 137 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.066687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048882 restraints weight = 38243.720| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.74 r_work: 0.2711 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11189 Z= 0.115 Angle : 0.527 13.635 15241 Z= 0.261 Chirality : 0.039 0.199 1709 Planarity : 0.003 0.038 1886 Dihedral : 10.540 102.330 1696 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.46 % Allowed : 24.32 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.04 (0.24), residues: 1296 helix: 1.90 (0.22), residues: 599 sheet: -0.62 (0.40), residues: 143 loop : -0.23 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.011 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.013 0.001 TRP C 144 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11189) covalent geometry : angle 0.52740 / 0.26 (15241) hydrogen bonds : bond 0.03485 / 2.32 ( 528) hydrogen bonds : angle 4.04579 / 2.91 ( 1432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.29 seconds wall clock time: 52 minutes 28.62 seconds (3148.62 seconds total)