Starting phenix.real_space_refine on Wed Sep 17 23:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jbf_61312/09_2025/9jbf_61312.map" } resolution = 3.21 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= 0.032 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 74 5.16 5 C 7882 2.51 5 N 1746 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11718 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 22, 'TRANS': 668} Chain breaks: 2 Chain: "B" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5443 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 22, 'TRANS': 668} Chain breaks: 2 Chain: "A" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 416 Unusual residues: {'3PE': 2, 'CLR': 1, 'PC1': 2, 'Y01': 2} Classifications: {'peptide': 2, 'undetermined': 7} Link IDs: {None: 8} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 416 Unusual residues: {'3PE': 2, 'CLR': 1, 'PC1': 2, 'Y01': 2} Classifications: {'peptide': 2, 'undetermined': 7} Link IDs: {None: 8} Time building chain proxies: 3.13, per 1000 atoms: 0.27 Number of scatterers: 11718 At special positions: 0 Unit cell: (102.616, 130.088, 96.96, 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 74 16.00 P 12 15.00 O 2004 8.00 N 1746 7.00 C 7882 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: 1.18 Conformation dependent library (CDL) restraints added in 555.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 2 sheets defined 79.9% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.800A pdb=" N ALA A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.158A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.771A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 124 removed outlier: 3.997A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.632A pdb=" N ALA A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 202 through 216 removed outlier: 4.434A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.557A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 4.255A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.510A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.517A pdb=" N PHE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 405 Processing helix chain 'A' and resid 409 through 434 removed outlier: 3.536A pdb=" N MET A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 474 removed outlier: 4.116A pdb=" N ILE A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 removed outlier: 4.372A pdb=" N ILE A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.689A pdb=" N PHE A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 542 removed outlier: 3.557A pdb=" N SER A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'A' and resid 654 through 682 removed outlier: 3.760A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 removed outlier: 3.984A pdb=" N PHE A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 758 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.671A pdb=" N ALA B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 4.094A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.526A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 124 removed outlier: 3.887A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.704A pdb=" N PHE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 167 through 196 removed outlier: 3.694A pdb=" N ALA B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 3.554A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.539A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.221A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.651A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.730A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.568A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.519A pdb=" N PHE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.581A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.763A pdb=" N MET B 370 " --> pdb=" O PHE B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.511A pdb=" N CYS B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 removed outlier: 4.233A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 502 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.780A pdb=" N PHE B 514 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 515 " --> pdb=" O SER B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 517 through 541 removed outlier: 3.529A pdb=" N THR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 removed outlier: 4.056A pdb=" N CYS B 638 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.824A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.828A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 701 removed outlier: 3.949A pdb=" N PHE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.679A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Processing helix chain 'B' and resid 758 through 764 removed outlier: 3.945A pdb=" N ARG B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 798 through 812 Processing sheet with id=AA1, first strand: chain 'A' and resid 781 through 782 Processing sheet with id=AA2, first strand: chain 'B' and resid 781 through 782 762 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1832 1.33 - 1.45: 3016 1.45 - 1.57: 6992 1.57 - 1.69: 24 1.69 - 1.81: 110 Bond restraints: 11974 Sorted by residual: bond pdb=" CA SER B 383 " pdb=" CB SER B 383 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.55e-02 4.16e+03 6.46e+00 bond pdb=" N PHE B 384 " pdb=" CA PHE B 384 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" N ILE B 386 " pdb=" CA ILE B 386 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.41e-02 5.03e+03 5.28e+00 bond pdb=" N SER B 387 " pdb=" CA SER B 387 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.24e-02 6.50e+03 5.08e+00 bond pdb=" N LEU B 648 " pdb=" CA LEU B 648 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.17e-02 7.31e+03 4.72e+00 ... (remaining 11969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 15790 2.02 - 4.05: 268 4.05 - 6.07: 67 6.07 - 8.10: 6 8.10 - 10.12: 5 Bond angle restraints: 16136 Sorted by residual: angle pdb=" N ILE B 386 " pdb=" CA ILE B 386 " pdb=" C ILE B 386 " ideal model delta sigma weight residual 112.04 107.50 4.54 1.40e+00 5.10e-01 1.05e+01 angle pdb=" CA GLN B 649 " pdb=" CB GLN B 649 " pdb=" CG GLN B 649 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.76e+00 angle pdb=" CA SER B 387 " pdb=" C SER B 387 " pdb=" O SER B 387 " ideal model delta sigma weight residual 120.55 117.35 3.20 1.07e+00 8.73e-01 8.95e+00 angle pdb=" N SER B 383 " pdb=" CA SER B 383 " pdb=" C SER B 383 " ideal model delta sigma weight residual 111.07 107.91 3.16 1.07e+00 8.73e-01 8.71e+00 angle pdb=" CA LEU A 533 " pdb=" CB LEU A 533 " pdb=" CG LEU A 533 " ideal model delta sigma weight residual 116.30 126.42 -10.12 3.50e+00 8.16e-02 8.36e+00 ... (remaining 16131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 7176 35.44 - 70.87: 354 70.87 - 106.30: 30 106.30 - 141.74: 10 141.74 - 177.17: 12 Dihedral angle restraints: 7582 sinusoidal: 3568 harmonic: 4014 Sorted by residual: dihedral pdb=" C17 P5S A 906 " pdb=" C20 P5S A 906 " pdb=" C21 P5S A 906 " pdb=" C22 P5S A 906 " ideal model delta sinusoidal sigma weight residual 71.45 -111.38 -177.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB P5S A 909 " pdb=" OG P5S A 909 " pdb=" P12 P5S A 909 " pdb=" O13 P5S A 909 " ideal model delta sinusoidal sigma weight residual 47.21 -124.09 171.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB P5S A 909 " pdb=" OG P5S A 909 " pdb=" P12 P5S A 909 " pdb=" O16 P5S A 909 " ideal model delta sinusoidal sigma weight residual 295.68 126.70 168.98 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 7579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1605 0.061 - 0.123: 220 0.123 - 0.184: 14 0.184 - 0.245: 1 0.245 - 0.307: 4 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C2 P5S B 908 " pdb=" C1 P5S B 908 " pdb=" C3 P5S B 908 " pdb=" O37 P5S B 908 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2 P5S A 906 " pdb=" C1 P5S A 906 " pdb=" C3 P5S A 906 " pdb=" O37 P5S A 906 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2 P5S A 909 " pdb=" C1 P5S A 909 " pdb=" C3 P5S A 909 " pdb=" O37 P5S A 909 " both_signs ideal model delta sigma weight residual False 2.59 2.31 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1841 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 371 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO A 372 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 371 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO B 372 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 55 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C CYS B 55 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS B 55 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY B 56 " -0.011 2.00e-02 2.50e+03 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 951 2.74 - 3.28: 12356 3.28 - 3.82: 19917 3.82 - 4.36: 23421 4.36 - 4.90: 40147 Nonbonded interactions: 96792 Sorted by model distance: nonbonded pdb=" O SER B 452 " pdb=" OG SER B 456 " model vdw 2.196 3.040 nonbonded pdb=" O HIS B 412 " pdb=" OG1 THR B 416 " model vdw 2.220 3.040 nonbonded pdb=" O SER A 452 " pdb=" OG SER A 456 " model vdw 2.227 3.040 nonbonded pdb=" OG SER B 797 " pdb=" OD1 ASP B 798 " model vdw 2.251 3.040 nonbonded pdb=" O LEU B 454 " pdb=" OG1 THR B 457 " model vdw 2.260 3.040 ... (remaining 96787 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 835) selection = (chain 'B' and resid 34 through 835) } 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: 5.340 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11974 Z= 0.173 Angle : 0.682 10.120 16136 Z= 0.338 Chirality : 0.044 0.307 1844 Planarity : 0.004 0.055 1888 Dihedral : 21.146 177.175 4994 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.33 % Allowed : 25.42 % Favored : 74.25 % 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 aren not related in a simple way. whole: 0.69 (0.23), residues: 1370 helix: 0.98 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 832 TYR 0.028 0.002 TYR B 320 PHE 0.032 0.001 PHE A 384 TRP 0.025 0.001 TRP A 460 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00371 (11974) covalent geometry : angle 0.68154 (16136) hydrogen bonds : bond 0.12518 ( 762) hydrogen bonds : angle 5.91823 ( 2253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 236 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7817 (t0) cc_final: 0.7608 (t0) REVERT: A 189 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 444 ILE cc_start: 0.8836 (mm) cc_final: 0.8627 (mm) REVERT: A 458 TYR cc_start: 0.7485 (m-10) cc_final: 0.6411 (m-10) REVERT: A 749 MET cc_start: 0.8548 (ttm) cc_final: 0.8237 (ttp) REVERT: B 189 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 193 TRP cc_start: 0.6806 (t60) cc_final: 0.6085 (t60) REVERT: B 203 LYS cc_start: 0.6033 (mtpt) cc_final: 0.5566 (pttp) REVERT: B 400 ILE cc_start: 0.7700 (mm) cc_final: 0.7482 (mm) REVERT: B 451 TYR cc_start: 0.6793 (m-80) cc_final: 0.6377 (m-80) REVERT: B 534 ILE cc_start: 0.8306 (mt) cc_final: 0.8068 (mm) REVERT: B 657 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7452 (mtp85) REVERT: B 752 GLN cc_start: 0.9250 (tp40) cc_final: 0.8895 (mm-40) REVERT: B 825 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7411 (ptp-170) outliers start: 4 outliers final: 0 residues processed: 236 average time/residue: 0.0941 time to fit residues: 33.7560 Evaluate side-chains 185 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 97 ASN A 181 ASN A 422 GLN A 520 GLN A 683 GLN A 693 GLN A 753 GLN B 89 ASN B 216 GLN B 422 GLN B 506 ASN B 520 GLN B 672 ASN B 683 GLN B 693 GLN B 716 HIS B 758 HIS B 811 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137889 restraints weight = 16002.384| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.00 r_work: 0.3592 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11974 Z= 0.146 Angle : 0.591 10.264 16136 Z= 0.296 Chirality : 0.041 0.149 1844 Planarity : 0.004 0.042 1888 Dihedral : 19.606 177.237 2506 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.90 % Allowed : 20.85 % Favored : 75.25 % 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 aren not related in a simple way. whole: 1.21 (0.23), residues: 1370 helix: 1.34 (0.16), residues: 1046 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.018 0.001 TYR A 451 PHE 0.024 0.001 PHE A 221 TRP 0.010 0.001 TRP A 460 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00330 (11974) covalent geometry : angle 0.59066 (16136) hydrogen bonds : bond 0.04915 ( 762) hydrogen bonds : angle 4.52186 ( 2253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 181 ASN cc_start: 0.7691 (t160) cc_final: 0.6955 (t0) REVERT: A 185 PHE cc_start: 0.8674 (m-10) cc_final: 0.8413 (m-80) REVERT: A 189 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 458 TYR cc_start: 0.7926 (m-10) cc_final: 0.6673 (m-10) REVERT: A 501 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 505 HIS cc_start: 0.5404 (OUTLIER) cc_final: 0.5186 (m-70) REVERT: B 193 TRP cc_start: 0.7010 (t60) cc_final: 0.6286 (t60) REVERT: B 203 LYS cc_start: 0.6091 (mtpt) cc_final: 0.5391 (pttp) REVERT: B 367 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6386 (t80) REVERT: B 451 TYR cc_start: 0.6999 (m-80) cc_final: 0.6501 (m-80) REVERT: B 501 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 534 ILE cc_start: 0.8405 (mt) cc_final: 0.8161 (mm) REVERT: B 657 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7564 (mtp85) REVERT: B 825 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7565 (mtt90) outliers start: 47 outliers final: 18 residues processed: 234 average time/residue: 0.0856 time to fit residues: 30.8105 Evaluate side-chains 198 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 674 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B 693 GLN B 753 GLN B 756 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137134 restraints weight = 16218.354| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.98 r_work: 0.3560 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11974 Z= 0.151 Angle : 0.582 9.492 16136 Z= 0.294 Chirality : 0.041 0.152 1844 Planarity : 0.004 0.041 1888 Dihedral : 18.633 177.301 2506 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.57 % Allowed : 20.27 % Favored : 76.16 % 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 aren not related in a simple way. whole: 1.26 (0.23), residues: 1370 helix: 1.38 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.88 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 759 TYR 0.019 0.001 TYR A 451 PHE 0.025 0.002 PHE A 221 TRP 0.010 0.001 TRP B 432 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00346 (11974) covalent geometry : angle 0.58232 (16136) hydrogen bonds : bond 0.04620 ( 762) hydrogen bonds : angle 4.35317 ( 2253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 451 TYR cc_start: 0.6778 (m-80) cc_final: 0.6430 (m-80) REVERT: A 458 TYR cc_start: 0.7865 (m-10) cc_final: 0.6605 (m-10) REVERT: A 501 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 505 HIS cc_start: 0.5352 (OUTLIER) cc_final: 0.5087 (m-70) REVERT: A 689 TYR cc_start: 0.7559 (t80) cc_final: 0.7245 (t80) REVERT: B 189 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 193 TRP cc_start: 0.7014 (t60) cc_final: 0.6262 (t60) REVERT: B 203 LYS cc_start: 0.6023 (mtpt) cc_final: 0.5605 (tttm) REVERT: B 367 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6210 (t80) REVERT: B 431 ILE cc_start: 0.8697 (mp) cc_final: 0.8410 (mp) REVERT: B 451 TYR cc_start: 0.7020 (m-80) cc_final: 0.6545 (m-80) REVERT: B 516 TYR cc_start: 0.6589 (m-10) cc_final: 0.6374 (m-10) REVERT: B 534 ILE cc_start: 0.8405 (mt) cc_final: 0.8185 (mm) REVERT: B 657 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7485 (mtp85) REVERT: B 823 GLU cc_start: 0.6701 (tt0) cc_final: 0.6349 (tt0) REVERT: B 830 PHE cc_start: 0.6854 (m-10) cc_final: 0.6639 (m-10) outliers start: 43 outliers final: 22 residues processed: 224 average time/residue: 0.0838 time to fit residues: 29.1079 Evaluate side-chains 198 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain B residue 793 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 693 GLN A 753 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN B 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.181198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137126 restraints weight = 16141.138| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.98 r_work: 0.3577 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11974 Z= 0.139 Angle : 0.557 8.601 16136 Z= 0.283 Chirality : 0.041 0.157 1844 Planarity : 0.004 0.038 1888 Dihedral : 17.984 177.156 2506 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.41 % Allowed : 20.93 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.23), residues: 1370 helix: 1.47 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 759 TYR 0.018 0.001 TYR A 451 PHE 0.025 0.001 PHE A 221 TRP 0.007 0.001 TRP A 432 HIS 0.004 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00317 (11974) covalent geometry : angle 0.55724 (16136) hydrogen bonds : bond 0.04439 ( 762) hydrogen bonds : angle 4.27207 ( 2253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7516 (mm-30) REVERT: A 451 TYR cc_start: 0.6788 (m-80) cc_final: 0.6379 (m-80) REVERT: A 458 TYR cc_start: 0.7849 (m-10) cc_final: 0.6551 (m-10) REVERT: A 501 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A 505 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.5134 (m-70) REVERT: B 193 TRP cc_start: 0.6990 (t60) cc_final: 0.6278 (t60) REVERT: B 203 LYS cc_start: 0.6061 (mtpt) cc_final: 0.5656 (tttm) REVERT: B 367 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5980 (t80) REVERT: B 431 ILE cc_start: 0.8712 (mp) cc_final: 0.8423 (mp) REVERT: B 451 TYR cc_start: 0.7014 (m-80) cc_final: 0.6574 (m-80) REVERT: B 516 TYR cc_start: 0.6701 (m-10) cc_final: 0.6487 (m-10) REVERT: B 644 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: B 657 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7457 (mtp85) REVERT: B 823 GLU cc_start: 0.6664 (tt0) cc_final: 0.6364 (tt0) REVERT: B 830 PHE cc_start: 0.6860 (m-10) cc_final: 0.6553 (m-10) outliers start: 41 outliers final: 24 residues processed: 211 average time/residue: 0.0872 time to fit residues: 28.8114 Evaluate side-chains 198 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 693 GLN A 753 GLN A 756 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137791 restraints weight = 16184.799| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.02 r_work: 0.3584 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11974 Z= 0.131 Angle : 0.553 8.546 16136 Z= 0.279 Chirality : 0.041 0.255 1844 Planarity : 0.004 0.036 1888 Dihedral : 17.395 177.309 2506 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.24 % Allowed : 21.84 % Favored : 74.92 % 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 aren not related in a simple way. whole: 1.48 (0.23), residues: 1370 helix: 1.57 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.95 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 759 TYR 0.018 0.001 TYR A 451 PHE 0.024 0.001 PHE A 221 TRP 0.009 0.001 TRP A 789 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00295 (11974) covalent geometry : angle 0.55332 (16136) hydrogen bonds : bond 0.04311 ( 762) hydrogen bonds : angle 4.21776 ( 2253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 458 TYR cc_start: 0.7524 (m-10) cc_final: 0.6496 (m-10) REVERT: A 501 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 505 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4862 (m-70) REVERT: B 193 TRP cc_start: 0.6875 (t60) cc_final: 0.6225 (t60) REVERT: B 203 LYS cc_start: 0.6031 (mtpt) cc_final: 0.5658 (tttm) REVERT: B 367 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.5978 (t80) REVERT: B 431 ILE cc_start: 0.8596 (mp) cc_final: 0.8298 (mp) REVERT: B 451 TYR cc_start: 0.6854 (m-80) cc_final: 0.6459 (m-80) REVERT: B 500 LEU cc_start: 0.8301 (tt) cc_final: 0.8061 (mt) REVERT: B 644 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: B 657 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7389 (mtp85) REVERT: B 823 GLU cc_start: 0.6690 (tt0) cc_final: 0.6399 (tt0) REVERT: B 830 PHE cc_start: 0.6835 (m-10) cc_final: 0.6568 (m-10) outliers start: 39 outliers final: 25 residues processed: 205 average time/residue: 0.0852 time to fit residues: 27.5792 Evaluate side-chains 190 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 693 GLN A 753 GLN A 756 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN B 753 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137667 restraints weight = 16173.087| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.02 r_work: 0.3581 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11974 Z= 0.132 Angle : 0.558 10.017 16136 Z= 0.279 Chirality : 0.041 0.171 1844 Planarity : 0.004 0.033 1888 Dihedral : 16.766 176.285 2506 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.24 % Allowed : 22.09 % Favored : 74.67 % 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 aren not related in a simple way. whole: 1.53 (0.23), residues: 1370 helix: 1.60 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 764 TYR 0.018 0.001 TYR A 451 PHE 0.024 0.001 PHE A 221 TRP 0.006 0.001 TRP A 396 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00300 (11974) covalent geometry : angle 0.55801 (16136) hydrogen bonds : bond 0.04231 ( 762) hydrogen bonds : angle 4.18898 ( 2253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 TYR cc_start: 0.7544 (m-10) cc_final: 0.6505 (m-10) REVERT: A 501 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8393 (mm) REVERT: B 189 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 193 TRP cc_start: 0.6860 (t60) cc_final: 0.6214 (t60) REVERT: B 203 LYS cc_start: 0.6111 (mtpt) cc_final: 0.5763 (tttm) REVERT: B 367 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.5889 (t80) REVERT: B 431 ILE cc_start: 0.8688 (mp) cc_final: 0.8408 (mp) REVERT: B 451 TYR cc_start: 0.6749 (m-80) cc_final: 0.6431 (m-80) REVERT: B 499 LEU cc_start: 0.8523 (tp) cc_final: 0.8207 (tp) REVERT: B 644 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: B 657 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7389 (mtp85) REVERT: B 689 TYR cc_start: 0.7381 (t80) cc_final: 0.7099 (t80) REVERT: B 823 GLU cc_start: 0.6750 (tt0) cc_final: 0.6461 (tt0) REVERT: B 830 PHE cc_start: 0.6857 (m-10) cc_final: 0.6617 (m-10) outliers start: 39 outliers final: 27 residues processed: 202 average time/residue: 0.0834 time to fit residues: 26.2348 Evaluate side-chains 192 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 137 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 753 GLN A 756 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.182243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138662 restraints weight = 16023.298| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.98 r_work: 0.3591 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11974 Z= 0.128 Angle : 0.553 7.790 16136 Z= 0.277 Chirality : 0.041 0.179 1844 Planarity : 0.004 0.032 1888 Dihedral : 16.140 179.291 2506 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.41 % Allowed : 21.51 % Favored : 75.08 % 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 aren not related in a simple way. whole: 1.54 (0.23), residues: 1370 helix: 1.62 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 764 TYR 0.018 0.001 TYR A 451 PHE 0.024 0.001 PHE A 708 TRP 0.007 0.001 TRP A 396 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00290 (11974) covalent geometry : angle 0.55299 (16136) hydrogen bonds : bond 0.04173 ( 762) hydrogen bonds : angle 4.18475 ( 2253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 458 TYR cc_start: 0.7570 (m-10) cc_final: 0.6522 (m-10) REVERT: A 501 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 149 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8766 (tp) REVERT: B 189 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 193 TRP cc_start: 0.6831 (t60) cc_final: 0.6208 (t60) REVERT: B 203 LYS cc_start: 0.6059 (mtpt) cc_final: 0.5762 (tttm) REVERT: B 211 LEU cc_start: 0.7861 (mm) cc_final: 0.7548 (mp) REVERT: B 367 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.5817 (t80) REVERT: B 431 ILE cc_start: 0.8707 (mp) cc_final: 0.8430 (mp) REVERT: B 499 LEU cc_start: 0.8511 (tp) cc_final: 0.8237 (tp) REVERT: B 644 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: B 657 ARG cc_start: 0.7600 (mtt90) cc_final: 0.7361 (mtp85) REVERT: B 823 GLU cc_start: 0.6805 (tt0) cc_final: 0.6493 (tt0) REVERT: B 825 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7392 (mtt90) REVERT: B 830 PHE cc_start: 0.6855 (m-10) cc_final: 0.6623 (m-10) outliers start: 41 outliers final: 26 residues processed: 203 average time/residue: 0.0929 time to fit residues: 29.1526 Evaluate side-chains 196 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 790 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 753 GLN A 756 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137654 restraints weight = 16101.717| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.01 r_work: 0.3577 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11974 Z= 0.136 Angle : 0.565 8.552 16136 Z= 0.284 Chirality : 0.041 0.187 1844 Planarity : 0.004 0.033 1888 Dihedral : 15.625 168.257 2506 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 21.76 % Favored : 74.67 % 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 aren not related in a simple way. whole: 1.63 (0.23), residues: 1370 helix: 1.67 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.75 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 764 TYR 0.018 0.001 TYR B 451 PHE 0.025 0.001 PHE A 221 TRP 0.007 0.001 TRP A 396 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd covalent geometry : bond 0.00314 (11974) covalent geometry : angle 0.56546 (16136) hydrogen bonds : bond 0.04210 ( 762) hydrogen bonds : angle 4.19452 ( 2253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 458 TYR cc_start: 0.7564 (m-10) cc_final: 0.6518 (m-10) REVERT: A 501 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8447 (mm) REVERT: B 149 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8801 (tp) REVERT: B 189 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 193 TRP cc_start: 0.6892 (t60) cc_final: 0.6209 (t60) REVERT: B 203 LYS cc_start: 0.6057 (mtpt) cc_final: 0.5769 (tttm) REVERT: B 211 LEU cc_start: 0.7863 (mm) cc_final: 0.7513 (mp) REVERT: B 367 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5863 (t80) REVERT: B 431 ILE cc_start: 0.8687 (mp) cc_final: 0.8418 (mp) REVERT: B 499 LEU cc_start: 0.8532 (tp) cc_final: 0.8286 (tp) REVERT: B 644 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: B 657 ARG cc_start: 0.7671 (mtt90) cc_final: 0.7362 (mtp85) REVERT: B 823 GLU cc_start: 0.6743 (tt0) cc_final: 0.6460 (tt0) REVERT: B 830 PHE cc_start: 0.6815 (m-10) cc_final: 0.6595 (m-10) outliers start: 43 outliers final: 31 residues processed: 206 average time/residue: 0.0846 time to fit residues: 27.2196 Evaluate side-chains 197 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 790 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 693 GLN A 753 GLN A 756 HIS B 63 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139427 restraints weight = 15951.910| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.00 r_work: 0.3608 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11974 Z= 0.124 Angle : 0.575 14.471 16136 Z= 0.285 Chirality : 0.041 0.187 1844 Planarity : 0.004 0.033 1888 Dihedral : 15.219 169.047 2506 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.16 % Allowed : 21.93 % Favored : 74.92 % 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 aren not related in a simple way. whole: 1.71 (0.23), residues: 1370 helix: 1.72 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 764 TYR 0.017 0.001 TYR A 451 PHE 0.026 0.001 PHE A 708 TRP 0.007 0.001 TRP A 432 HIS 0.007 0.001 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00276 (11974) covalent geometry : angle 0.57542 (16136) hydrogen bonds : bond 0.04099 ( 762) hydrogen bonds : angle 4.18831 ( 2253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B 189 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 193 TRP cc_start: 0.6914 (t60) cc_final: 0.6211 (t60) REVERT: B 203 LYS cc_start: 0.6086 (mtpt) cc_final: 0.5762 (tttm) REVERT: B 211 LEU cc_start: 0.7899 (mm) cc_final: 0.7497 (mp) REVERT: B 367 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.5808 (t80) REVERT: B 431 ILE cc_start: 0.8777 (mp) cc_final: 0.8513 (mp) REVERT: B 644 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: B 657 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7237 (mtp85) REVERT: B 752 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8797 (tp40) REVERT: B 821 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6811 (mp0) REVERT: B 823 GLU cc_start: 0.6744 (tt0) cc_final: 0.6449 (tt0) REVERT: B 825 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7551 (mtt90) REVERT: B 830 PHE cc_start: 0.6743 (m-10) cc_final: 0.6478 (m-10) outliers start: 38 outliers final: 26 residues processed: 192 average time/residue: 0.0933 time to fit residues: 27.5739 Evaluate side-chains 189 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 790 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN A 756 HIS B 63 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.181459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137353 restraints weight = 16048.704| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.00 r_work: 0.3574 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11974 Z= 0.149 Angle : 0.594 12.106 16136 Z= 0.297 Chirality : 0.042 0.244 1844 Planarity : 0.004 0.033 1888 Dihedral : 15.151 174.606 2506 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.91 % Allowed : 22.34 % Favored : 74.75 % 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 aren not related in a simple way. whole: 1.42 (0.23), residues: 1370 helix: 1.53 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.017 0.001 TYR A 451 PHE 0.025 0.001 PHE A 221 TRP 0.008 0.001 TRP A 396 HIS 0.012 0.001 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00350 (11974) covalent geometry : angle 0.59445 (16136) hydrogen bonds : bond 0.04245 ( 762) hydrogen bonds : angle 4.22999 ( 2253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 193 TRP cc_start: 0.6891 (t60) cc_final: 0.6201 (t60) REVERT: B 203 LYS cc_start: 0.6064 (mtpt) cc_final: 0.5816 (tttm) REVERT: B 211 LEU cc_start: 0.7823 (mm) cc_final: 0.7419 (mp) REVERT: B 367 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.5882 (t80) REVERT: B 431 ILE cc_start: 0.8668 (mp) cc_final: 0.8405 (mp) REVERT: B 644 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: B 657 ARG cc_start: 0.7711 (mtt90) cc_final: 0.7287 (mtp85) REVERT: B 689 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7300 (t80) REVERT: B 821 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6708 (mp0) REVERT: B 823 GLU cc_start: 0.6833 (tt0) cc_final: 0.6514 (tt0) REVERT: B 825 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7412 (mtt90) outliers start: 35 outliers final: 28 residues processed: 190 average time/residue: 0.0921 time to fit residues: 27.1766 Evaluate side-chains 188 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 PHE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 654 GLN Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 790 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN A 756 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141026 restraints weight = 15982.602| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.15 r_work: 0.3603 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11974 Z= 0.124 Angle : 0.577 12.139 16136 Z= 0.288 Chirality : 0.042 0.234 1844 Planarity : 0.003 0.034 1888 Dihedral : 14.892 178.232 2506 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.82 % Allowed : 22.43 % Favored : 74.75 % 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 aren not related in a simple way. whole: 1.68 (0.23), residues: 1370 helix: 1.72 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.017 0.001 TYR A 451 PHE 0.026 0.001 PHE A 708 TRP 0.009 0.001 TRP A 679 HIS 0.011 0.001 HIS A 756 Details of bonding type rmsd covalent geometry : bond 0.00276 (11974) covalent geometry : angle 0.57714 (16136) hydrogen bonds : bond 0.04081 ( 762) hydrogen bonds : angle 4.17214 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.87 seconds wall clock time: 54 minutes 32.79 seconds (3272.79 seconds total)