Starting phenix.real_space_refine on Thu Jul 2 18:45:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.cif" model { file = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2026/7e2i_30958.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1208 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 67 5.16 5 C 5595 2.51 5 N 1354 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8569 Number of models: 1 Model: "" Number of chains: 4 Chain: "G" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7058 Classifications: {'peptide': 907} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 37, 'TRANS': 869} Chain breaks: 4 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 301 Unusual residues: {'NAG': 4, 'Y01': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.50, per 1000 atoms: 0.18 Number of scatterers: 8569 At special positions: 0 Unit cell: (109.172, 115.856, 115.856, 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) Zn 1 29.99 S 67 16.00 O 1552 8.00 N 1354 7.00 C 5595 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 Links applied NAG-ASN " NAG D1608 " - " ASN D 476 " " NAG D1610 " - " ASN D 917 " " NAG D1611 " - " ASN D 836 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 194.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 140 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 182 " 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 5 sheets defined 55.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'G' and resid 71 through 74 Processing helix chain 'G' and resid 100 through 117 removed outlier: 3.604A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 143 removed outlier: 3.754A pdb=" N GLU G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 168 removed outlier: 3.592A pdb=" N GLY G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 4.083A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 182 through 186' Processing helix chain 'D' and resid 189 through 210 Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 372 through 388 removed outlier: 3.505A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'D' and resid 463 through 472 removed outlier: 4.479A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 503 removed outlier: 4.366A pdb=" N GLN D 497 " --> pdb=" O HIS D 493 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 522 removed outlier: 3.518A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 548 Processing helix chain 'D' and resid 558 through 587 removed outlier: 3.834A pdb=" N LEU D 563 " --> pdb=" O ASN D 559 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 623 removed outlier: 5.132A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER D 607 " --> pdb=" O HIS D 603 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 659 removed outlier: 4.537A pdb=" N PHE D 633 " --> pdb=" O ALA D 629 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 688 through 718 removed outlier: 5.084A pdb=" N LEU D 710 " --> pdb=" O PHE D 706 " (cutoff:3.500A) Proline residue: D 711 - end of helix Processing helix chain 'D' and resid 719 through 738 Processing helix chain 'D' and resid 748 through 752 removed outlier: 3.676A pdb=" N PHE D 752 " --> pdb=" O LEU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 765 removed outlier: 4.261A pdb=" N ASP D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 771 Processing helix chain 'D' and resid 772 through 779 Processing helix chain 'D' and resid 820 through 835 Processing helix chain 'D' and resid 851 through 860 removed outlier: 4.006A pdb=" N THR D 855 " --> pdb=" O CYS D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 902 removed outlier: 4.347A pdb=" N LYS D 891 " --> pdb=" O GLU D 887 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 892 " --> pdb=" O LEU D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 953 removed outlier: 3.965A pdb=" N MET D 940 " --> pdb=" O ALA D 936 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER D 953 " --> pdb=" O SER D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 1004 Processing helix chain 'D' and resid 1005 through 1030 Processing helix chain 'D' and resid 1036 through 1059 removed outlier: 4.479A pdb=" N VAL D1040 " --> pdb=" O VAL D1036 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR D1041 " --> pdb=" O LEU D1037 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D1042 " --> pdb=" O GLU D1038 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D1043 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D1046 " --> pdb=" O ILE D1042 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D1047 " --> pdb=" O SER D1043 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D1051 " --> pdb=" O GLY D1047 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE D1052 " --> pdb=" O LEU D1048 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D1053 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS D1055 " --> pdb=" O ASN D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1098 removed outlier: 3.520A pdb=" N VAL D1072 " --> pdb=" O ARG D1068 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D1073 " --> pdb=" O GLU D1069 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER D1081 " --> pdb=" O SER D1077 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA D1082 " --> pdb=" O ARG D1078 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR D1090 " --> pdb=" O ALA D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1133 removed outlier: 3.792A pdb=" N THR D1106 " --> pdb=" O VAL D1102 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS D1131 " --> pdb=" O PHE D1127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 76 through 78 Processing sheet with id=AA2, first strand: chain 'G' and resid 85 through 86 removed outlier: 7.775A pdb=" N ILE G 85 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N GLU G 126 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP G 147 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 451 through 459 removed outlier: 4.668A pdb=" N SER D 301 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ARG D 302 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 487 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 304 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 788 through 789 Processing sheet with id=AA5, first strand: chain 'D' and resid 913 through 914 removed outlier: 6.290A pdb=" N ARG D 913 " --> pdb=" O ARG D 921 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1254 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: 1.04 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1356 1.32 - 1.44: 2434 1.44 - 1.57: 4908 1.57 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 8801 Sorted by residual: bond pdb=" CB TRP D 966 " pdb=" CG TRP D 966 " ideal model delta sigma weight residual 1.498 1.414 0.084 3.10e-02 1.04e+03 7.31e+00 bond pdb=" C MET D 785 " pdb=" N PRO D 786 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.20e-02 6.94e+03 4.85e+00 bond pdb=" C SER D 758 " pdb=" N HIS D 759 " ideal model delta sigma weight residual 1.331 1.287 0.044 2.07e-02 2.33e+03 4.57e+00 bond pdb=" CG ASN D 476 " pdb=" ND2 ASN D 476 " ideal model delta sigma weight residual 1.328 1.369 -0.041 2.10e-02 2.27e+03 3.90e+00 bond pdb=" C LEU D 749 " pdb=" N SER D 750 " ideal model delta sigma weight residual 1.331 1.301 0.031 1.62e-02 3.81e+03 3.57e+00 ... (remaining 8796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11391 1.63 - 3.26: 511 3.26 - 4.88: 75 4.88 - 6.51: 19 6.51 - 8.14: 9 Bond angle restraints: 12005 Sorted by residual: angle pdb=" N PHE D 255 " pdb=" CA PHE D 255 " pdb=" C PHE D 255 " ideal model delta sigma weight residual 108.19 116.33 -8.14 1.29e+00 6.01e-01 3.98e+01 angle pdb=" N PRO D 254 " pdb=" CA PRO D 254 " pdb=" C PRO D 254 " ideal model delta sigma weight residual 112.47 120.58 -8.11 2.06e+00 2.36e-01 1.55e+01 angle pdb=" C PRO D 254 " pdb=" N PHE D 255 " pdb=" CA PHE D 255 " ideal model delta sigma weight residual 122.08 115.53 6.55 1.84e+00 2.95e-01 1.27e+01 angle pdb=" C LEU D 749 " pdb=" N SER D 750 " pdb=" CA SER D 750 " ideal model delta sigma weight residual 122.31 115.38 6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" C PHE D 554 " pdb=" N PHE D 555 " pdb=" CA PHE D 555 " ideal model delta sigma weight residual 121.80 113.75 8.05 2.44e+00 1.68e-01 1.09e+01 ... (remaining 12000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4502 16.97 - 33.95: 469 33.95 - 50.92: 71 50.92 - 67.90: 21 67.90 - 84.87: 5 Dihedral angle restraints: 5068 sinusoidal: 1962 harmonic: 3106 Sorted by residual: dihedral pdb=" CA SER D 290 " pdb=" C SER D 290 " pdb=" N PHE D 291 " pdb=" CA PHE D 291 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR D 253 " pdb=" C TYR D 253 " pdb=" N PRO D 254 " pdb=" CA PRO D 254 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PHE D1127 " pdb=" C PHE D1127 " pdb=" N GLN D1128 " pdb=" CA GLN D1128 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1367 0.132 - 0.264: 14 0.264 - 0.396: 0 0.396 - 0.529: 1 0.529 - 0.661: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" C1 NAG D1610 " pdb=" ND2 ASN D 917 " pdb=" C2 NAG D1610 " pdb=" O5 NAG D1610 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG D1611 " pdb=" ND2 ASN D 836 " pdb=" C2 NAG D1611 " pdb=" O5 NAG D1611 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA PRO D 254 " pdb=" N PRO D 254 " pdb=" C PRO D 254 " pdb=" CB PRO D 254 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1380 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 883 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C GLN D 883 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN D 883 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 884 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 456 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 457 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 457 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 457 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 291 " 0.004 2.00e-02 2.50e+03 1.26e-02 2.79e+00 pdb=" CG PHE D 291 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE D 291 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 291 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 291 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE D 291 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 291 " -0.002 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 166 2.63 - 3.19: 9307 3.19 - 3.76: 13529 3.76 - 4.33: 17745 4.33 - 4.90: 26852 Nonbonded interactions: 67599 Sorted by model distance: nonbonded pdb=" O PRO D 350 " pdb=" ND2 ASN D 356 " model vdw 2.056 3.120 nonbonded pdb=" OD1 ASP G 147 " pdb="ZN ZN G 501 " model vdw 2.074 2.230 nonbonded pdb=" OE1 GLU G 176 " pdb="ZN ZN G 501 " model vdw 2.094 2.230 nonbonded pdb=" O ALA D1059 " pdb=" OG SER D1075 " model vdw 2.105 3.040 nonbonded pdb=" O GLU G 53 " pdb=" OG SER G 59 " model vdw 2.106 3.040 ... (remaining 67594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.007 0.242 8806 Z= 0.309 Angle : 0.839 12.751 12014 Z= 0.443 Chirality : 0.051 0.661 1383 Planarity : 0.005 0.047 1465 Dihedral : 14.315 84.873 3056 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.66 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.21), residues: 1046 helix: -2.23 (0.18), residues: 534 sheet: -3.19 (0.67), residues: 52 loop : -3.60 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 329 TYR 0.017 0.002 TYR D1060 PHE 0.024 0.002 PHE D 967 TRP 0.022 0.002 TRP D1120 HIS 0.005 0.001 HIS D 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 ( 8801) covalent geometry : angle 0.82031 / 0.44 (12005) hydrogen bonds : bond 0.13384 / 8.62 ( 425) hydrogen bonds : angle 6.73104 / 4.68 ( 1254) metal coordination : bond 0.21484 / 10.93 ( 2) link_NAG-ASN : bond 0.02200 / 1.10 ( 3) link_NAG-ASN : angle 6.50268 / 2.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 81 ASN cc_start: 0.8670 (t0) cc_final: 0.8455 (t0) REVERT: G 98 MET cc_start: 0.8708 (ptm) cc_final: 0.8233 (ptp) REVERT: G 102 CYS cc_start: 0.9143 (t) cc_final: 0.8353 (t) REVERT: G 141 TYR cc_start: 0.8299 (m-10) cc_final: 0.7834 (m-10) REVERT: G 154 ASP cc_start: 0.8478 (m-30) cc_final: 0.8256 (m-30) REVERT: G 175 TYR cc_start: 0.7553 (t80) cc_final: 0.6516 (t80) REVERT: G 186 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8247 (ttmt) REVERT: G 188 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 343 THR cc_start: 0.7712 (t) cc_final: 0.7454 (m) REVERT: D 460 LYS cc_start: 0.9241 (pttm) cc_final: 0.8865 (pttm) REVERT: D 502 MET cc_start: 0.8768 (tmm) cc_final: 0.8526 (tmm) REVERT: D 530 MET cc_start: 0.8998 (tpp) cc_final: 0.8459 (tpp) REVERT: D 595 GLU cc_start: 0.8961 (mp0) cc_final: 0.8512 (mp0) REVERT: D 641 ILE cc_start: 0.9617 (tp) cc_final: 0.9379 (tp) REVERT: D 753 GLN cc_start: 0.8912 (pt0) cc_final: 0.8634 (pt0) REVERT: D 796 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8031 (tm-30) REVERT: D 896 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8030 (mt-10) REVERT: D 926 GLU cc_start: 0.8271 (pm20) cc_final: 0.8006 (pm20) REVERT: D 1011 TYR cc_start: 0.9243 (m-80) cc_final: 0.8795 (m-80) REVERT: D 1097 MET cc_start: 0.9178 (ttm) cc_final: 0.8868 (tmm) REVERT: D 1126 PHE cc_start: 0.8840 (t80) cc_final: 0.8417 (t80) REVERT: D 1128 GLN cc_start: 0.9315 (mp10) cc_final: 0.9031 (mp10) REVERT: D 1129 CYS cc_start: 0.9471 (t) cc_final: 0.9000 (t) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.0708 time to fit residues: 26.0669 Evaluate side-chains 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 overall best weight: 2.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 252 ASN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN D 356 ASN D 362 ASN D 363 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 ASN ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 842 GLN D 964 ASN D 977 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.113010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087277 restraints weight = 22928.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088697 restraints weight = 12548.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089683 restraints weight = 8635.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090097 restraints weight = 7260.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090293 restraints weight = 6525.868| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8806 Z= 0.168 Angle : 0.707 9.371 12014 Z= 0.362 Chirality : 0.043 0.260 1383 Planarity : 0.005 0.042 1465 Dihedral : 7.117 59.804 1220 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.22 % Allowed : 6.75 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.25), residues: 1046 helix: -0.50 (0.21), residues: 539 sheet: -3.13 (0.64), residues: 56 loop : -2.98 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 61 TYR 0.013 0.001 TYR G 80 PHE 0.023 0.002 PHE D 291 TRP 0.018 0.001 TRP D 651 HIS 0.004 0.001 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 8801) covalent geometry : angle 0.70132 / 0.36 (12005) hydrogen bonds : bond 0.04776 / 3.03 ( 425) hydrogen bonds : angle 5.25649 / 3.57 ( 1254) metal coordination : bond 0.00502 / 0.26 ( 2) link_NAG-ASN : bond 0.00675 / 0.35 ( 3) link_NAG-ASN : angle 3.37727 / 1.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 98 MET cc_start: 0.8474 (ptm) cc_final: 0.8207 (ptp) REVERT: G 106 LEU cc_start: 0.9442 (tt) cc_final: 0.9165 (pp) REVERT: G 141 TYR cc_start: 0.8275 (m-10) cc_final: 0.7875 (m-10) REVERT: G 154 ASP cc_start: 0.8369 (m-30) cc_final: 0.8155 (m-30) REVERT: G 184 SER cc_start: 0.8622 (p) cc_final: 0.8397 (p) REVERT: G 186 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8207 (ttmt) REVERT: D 198 MET cc_start: 0.8692 (tmm) cc_final: 0.8322 (tmm) REVERT: D 453 MET cc_start: 0.9059 (tmm) cc_final: 0.8106 (tmm) REVERT: D 454 LEU cc_start: 0.8514 (tp) cc_final: 0.7823 (tp) REVERT: D 460 LYS cc_start: 0.9211 (pttp) cc_final: 0.8957 (pttm) REVERT: D 502 MET cc_start: 0.8528 (tmm) cc_final: 0.8103 (tpp) REVERT: D 518 MET cc_start: 0.8817 (mtm) cc_final: 0.8570 (mtm) REVERT: D 530 MET cc_start: 0.9122 (tpp) cc_final: 0.8419 (tpp) REVERT: D 554 PHE cc_start: 0.8510 (t80) cc_final: 0.8161 (t80) REVERT: D 575 PHE cc_start: 0.8873 (m-10) cc_final: 0.8109 (m-80) REVERT: D 579 ASP cc_start: 0.8863 (m-30) cc_final: 0.8625 (m-30) REVERT: D 796 GLU cc_start: 0.8976 (mt-10) cc_final: 0.7967 (tm-30) REVERT: D 926 GLU cc_start: 0.8047 (pm20) cc_final: 0.7690 (pm20) REVERT: D 996 PHE cc_start: 0.8714 (t80) cc_final: 0.8490 (t80) REVERT: D 1011 TYR cc_start: 0.8986 (m-80) cc_final: 0.8636 (m-80) REVERT: D 1085 MET cc_start: 0.8854 (tpp) cc_final: 0.8409 (tpp) REVERT: D 1126 PHE cc_start: 0.8720 (t80) cc_final: 0.8285 (t80) outliers start: 2 outliers final: 1 residues processed: 247 average time/residue: 0.0669 time to fit residues: 23.9695 Evaluate side-chains 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 362 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1107 GLN D1128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085986 restraints weight = 22860.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088493 restraints weight = 11615.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090216 restraints weight = 7668.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090339 restraints weight = 6620.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090468 restraints weight = 5849.216| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8806 Z= 0.189 Angle : 0.713 9.323 12014 Z= 0.365 Chirality : 0.043 0.245 1383 Planarity : 0.005 0.042 1465 Dihedral : 7.136 58.766 1220 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.26), residues: 1046 helix: 0.07 (0.22), residues: 537 sheet: -3.37 (0.61), residues: 57 loop : -2.77 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 61 TYR 0.011 0.001 TYR G 175 PHE 0.020 0.002 PHE D 533 TRP 0.013 0.001 TRP D 651 HIS 0.004 0.001 HIS D1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 8801) covalent geometry : angle 0.70624 / 0.36 (12005) hydrogen bonds : bond 0.04702 / 3.00 ( 425) hydrogen bonds : angle 5.16835 / 3.52 ( 1254) metal coordination : bond 0.00204 / 0.10 ( 2) link_NAG-ASN : bond 0.00699 / 0.36 ( 3) link_NAG-ASN : angle 3.55002 / 1.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9230 (m-10) cc_final: 0.8823 (m-80) REVERT: G 141 TYR cc_start: 0.8296 (m-10) cc_final: 0.7884 (m-10) REVERT: G 150 THR cc_start: 0.7705 (t) cc_final: 0.7480 (t) REVERT: G 157 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7899 (tptt) REVERT: G 184 SER cc_start: 0.9111 (p) cc_final: 0.8540 (p) REVERT: G 186 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8097 (tmtt) REVERT: D 198 MET cc_start: 0.8649 (tmm) cc_final: 0.8269 (tmm) REVERT: D 453 MET cc_start: 0.9127 (tmm) cc_final: 0.8172 (tmm) REVERT: D 454 LEU cc_start: 0.8599 (tp) cc_final: 0.7952 (tp) REVERT: D 460 LYS cc_start: 0.9125 (pttp) cc_final: 0.8822 (pttm) REVERT: D 465 MET cc_start: 0.8721 (ttt) cc_final: 0.8496 (tpp) REVERT: D 502 MET cc_start: 0.8520 (tmm) cc_final: 0.8082 (tpp) REVERT: D 518 MET cc_start: 0.8866 (mtm) cc_final: 0.8624 (mtm) REVERT: D 530 MET cc_start: 0.9084 (tpp) cc_final: 0.8251 (tpp) REVERT: D 554 PHE cc_start: 0.8361 (t80) cc_final: 0.8079 (t80) REVERT: D 575 PHE cc_start: 0.8885 (m-10) cc_final: 0.8161 (m-80) REVERT: D 579 ASP cc_start: 0.8782 (m-30) cc_final: 0.8555 (m-30) REVERT: D 595 GLU cc_start: 0.9067 (pt0) cc_final: 0.8860 (mp0) REVERT: D 794 SER cc_start: 0.9281 (p) cc_final: 0.8441 (m) REVERT: D 796 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8685 (mp0) REVERT: D 805 LYS cc_start: 0.9152 (pttm) cc_final: 0.8912 (pttm) REVERT: D 812 LEU cc_start: 0.9208 (pp) cc_final: 0.8618 (pp) REVERT: D 926 GLU cc_start: 0.8046 (pm20) cc_final: 0.7681 (pm20) REVERT: D 966 TRP cc_start: 0.7880 (m100) cc_final: 0.7083 (m100) REVERT: D 1011 TYR cc_start: 0.9121 (m-80) cc_final: 0.8686 (m-80) REVERT: D 1085 MET cc_start: 0.8945 (tpp) cc_final: 0.8478 (tpp) REVERT: D 1126 PHE cc_start: 0.8796 (t80) cc_final: 0.8330 (t80) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.0680 time to fit residues: 24.4497 Evaluate side-chains 212 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 72 optimal weight: 0.0020 chunk 24 optimal weight: 0.0270 chunk 63 optimal weight: 10.0000 overall best weight: 1.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089671 restraints weight = 22674.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092080 restraints weight = 11740.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094467 restraints weight = 7461.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094305 restraints weight = 6400.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094526 restraints weight = 5560.653| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8806 Z= 0.141 Angle : 0.675 9.128 12014 Z= 0.341 Chirality : 0.041 0.225 1383 Planarity : 0.004 0.042 1465 Dihedral : 6.829 57.593 1220 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.26), residues: 1046 helix: 0.43 (0.22), residues: 528 sheet: -3.10 (0.65), residues: 51 loop : -2.55 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 61 TYR 0.016 0.001 TYR D 499 PHE 0.018 0.001 PHE D 455 TRP 0.014 0.001 TRP D 651 HIS 0.004 0.001 HIS D1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8801) covalent geometry : angle 0.66855 / 0.34 (12005) hydrogen bonds : bond 0.04377 / 2.78 ( 425) hydrogen bonds : angle 4.88905 / 3.32 ( 1254) metal coordination : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : bond 0.00780 / 0.41 ( 3) link_NAG-ASN : angle 3.58331 / 1.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9274 (m-10) cc_final: 0.8985 (m-10) REVERT: G 141 TYR cc_start: 0.8169 (m-10) cc_final: 0.7729 (m-10) REVERT: G 150 THR cc_start: 0.7957 (t) cc_final: 0.7662 (t) REVERT: G 175 TYR cc_start: 0.7095 (t80) cc_final: 0.6446 (t80) REVERT: G 186 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8003 (tmtt) REVERT: D 198 MET cc_start: 0.8774 (tmm) cc_final: 0.8311 (tmm) REVERT: D 460 LYS cc_start: 0.9120 (pttp) cc_final: 0.8749 (pttm) REVERT: D 502 MET cc_start: 0.8444 (tmm) cc_final: 0.7952 (tpp) REVERT: D 518 MET cc_start: 0.8850 (mtm) cc_final: 0.8590 (mtm) REVERT: D 530 MET cc_start: 0.9114 (tpp) cc_final: 0.8275 (tpp) REVERT: D 554 PHE cc_start: 0.8215 (t80) cc_final: 0.7946 (t80) REVERT: D 575 PHE cc_start: 0.8887 (m-10) cc_final: 0.8152 (m-80) REVERT: D 579 ASP cc_start: 0.8685 (m-30) cc_final: 0.8453 (m-30) REVERT: D 595 GLU cc_start: 0.9066 (pt0) cc_final: 0.8860 (mp0) REVERT: D 796 GLU cc_start: 0.8955 (mt-10) cc_final: 0.7924 (tm-30) REVERT: D 805 LYS cc_start: 0.9124 (pttm) cc_final: 0.8915 (pttm) REVERT: D 926 GLU cc_start: 0.7925 (pm20) cc_final: 0.7547 (pm20) REVERT: D 1006 ILE cc_start: 0.9061 (mp) cc_final: 0.8664 (mt) REVERT: D 1011 TYR cc_start: 0.9096 (m-80) cc_final: 0.8647 (m-80) REVERT: D 1126 PHE cc_start: 0.8856 (t80) cc_final: 0.8426 (t80) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.0673 time to fit residues: 23.6373 Evaluate side-chains 208 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 80 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 362 ASN D 572 ASN D 659 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.112321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086120 restraints weight = 22863.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088523 restraints weight = 11630.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.089331 restraints weight = 8027.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089572 restraints weight = 7002.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089878 restraints weight = 6474.765| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8806 Z= 0.231 Angle : 0.746 11.184 12014 Z= 0.380 Chirality : 0.043 0.241 1383 Planarity : 0.005 0.049 1465 Dihedral : 7.095 58.565 1220 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.26), residues: 1046 helix: 0.37 (0.22), residues: 537 sheet: -3.14 (0.64), residues: 51 loop : -2.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 329 TYR 0.015 0.001 TYR D 734 PHE 0.019 0.002 PHE D 555 TRP 0.016 0.002 TRP D 651 HIS 0.013 0.001 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 ( 8801) covalent geometry : angle 0.73847 / 0.38 (12005) hydrogen bonds : bond 0.04682 / 2.98 ( 425) hydrogen bonds : angle 5.06250 / 3.43 ( 1254) metal coordination : bond 0.01623 / 0.77 ( 2) link_NAG-ASN : bond 0.00706 / 0.37 ( 3) link_NAG-ASN : angle 3.90566 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9276 (m-10) cc_final: 0.9011 (m-10) REVERT: G 141 TYR cc_start: 0.8138 (m-10) cc_final: 0.7760 (m-10) REVERT: G 150 THR cc_start: 0.7931 (t) cc_final: 0.7624 (t) REVERT: G 175 TYR cc_start: 0.7028 (t80) cc_final: 0.6420 (t80) REVERT: D 198 MET cc_start: 0.8736 (tmm) cc_final: 0.8526 (tmm) REVERT: D 291 PHE cc_start: 0.8252 (p90) cc_final: 0.7889 (p90) REVERT: D 460 LYS cc_start: 0.9176 (pttp) cc_final: 0.8902 (pttm) REVERT: D 502 MET cc_start: 0.8310 (tmm) cc_final: 0.7829 (tpp) REVERT: D 530 MET cc_start: 0.9096 (tpp) cc_final: 0.8339 (tpp) REVERT: D 554 PHE cc_start: 0.8012 (t80) cc_final: 0.7464 (t80) REVERT: D 575 PHE cc_start: 0.8890 (m-10) cc_final: 0.8220 (m-80) REVERT: D 579 ASP cc_start: 0.8751 (m-30) cc_final: 0.8544 (m-30) REVERT: D 796 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8742 (mp0) REVERT: D 805 LYS cc_start: 0.9157 (pttm) cc_final: 0.8876 (pttm) REVERT: D 812 LEU cc_start: 0.9328 (pp) cc_final: 0.8628 (pp) REVERT: D 926 GLU cc_start: 0.8032 (pm20) cc_final: 0.7643 (pm20) REVERT: D 1011 TYR cc_start: 0.9085 (m-10) cc_final: 0.8727 (m-80) REVERT: D 1126 PHE cc_start: 0.8851 (t80) cc_final: 0.8489 (t80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.0656 time to fit residues: 22.5407 Evaluate side-chains 199 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 0.0030 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.0370 chunk 52 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 572 ASN D 778 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088661 restraints weight = 22197.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091137 restraints weight = 10695.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091690 restraints weight = 7558.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091998 restraints weight = 6840.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092289 restraints weight = 6161.208| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8806 Z= 0.170 Angle : 0.708 10.596 12014 Z= 0.360 Chirality : 0.042 0.235 1383 Planarity : 0.004 0.044 1465 Dihedral : 6.990 59.608 1220 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1046 helix: 0.45 (0.23), residues: 527 sheet: -3.04 (0.64), residues: 51 loop : -2.48 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 61 TYR 0.010 0.001 TYR D 468 PHE 0.033 0.002 PHE D 996 TRP 0.016 0.001 TRP D 651 HIS 0.013 0.001 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 8801) covalent geometry : angle 0.70128 / 0.36 (12005) hydrogen bonds : bond 0.04507 / 2.87 ( 425) hydrogen bonds : angle 4.96355 / 3.37 ( 1254) metal coordination : bond 0.03866 / 1.94 ( 2) link_NAG-ASN : bond 0.00764 / 0.40 ( 3) link_NAG-ASN : angle 3.67243 / 1.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 65 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8086 (mmmt) REVERT: G 80 TYR cc_start: 0.9270 (m-10) cc_final: 0.9001 (m-10) REVERT: G 98 MET cc_start: 0.8624 (ppp) cc_final: 0.8286 (ppp) REVERT: G 139 LEU cc_start: 0.8488 (mm) cc_final: 0.8134 (mm) REVERT: G 141 TYR cc_start: 0.8033 (m-10) cc_final: 0.7590 (m-10) REVERT: G 150 THR cc_start: 0.7904 (t) cc_final: 0.7567 (t) REVERT: G 175 TYR cc_start: 0.6978 (t80) cc_final: 0.6533 (t80) REVERT: D 198 MET cc_start: 0.8728 (tmm) cc_final: 0.8288 (tmm) REVERT: D 291 PHE cc_start: 0.8114 (p90) cc_final: 0.7736 (p90) REVERT: D 460 LYS cc_start: 0.9183 (pttp) cc_final: 0.8911 (pttm) REVERT: D 502 MET cc_start: 0.8353 (tmm) cc_final: 0.7905 (tpp) REVERT: D 530 MET cc_start: 0.9071 (tpp) cc_final: 0.8367 (tpp) REVERT: D 554 PHE cc_start: 0.8242 (t80) cc_final: 0.7718 (t80) REVERT: D 575 PHE cc_start: 0.8868 (m-10) cc_final: 0.8641 (m-10) REVERT: D 595 GLU cc_start: 0.8963 (mp0) cc_final: 0.8489 (mp0) REVERT: D 739 ASN cc_start: 0.7664 (t0) cc_final: 0.7150 (t0) REVERT: D 796 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8707 (mp0) REVERT: D 805 LYS cc_start: 0.9132 (pttm) cc_final: 0.8865 (pttm) REVERT: D 812 LEU cc_start: 0.9289 (pp) cc_final: 0.8601 (pp) REVERT: D 926 GLU cc_start: 0.8035 (pm20) cc_final: 0.7663 (pm20) REVERT: D 966 TRP cc_start: 0.7889 (m100) cc_final: 0.7203 (m100) REVERT: D 1011 TYR cc_start: 0.8958 (m-10) cc_final: 0.8656 (m-80) REVERT: D 1126 PHE cc_start: 0.8787 (t80) cc_final: 0.8483 (t80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0667 time to fit residues: 23.6508 Evaluate side-chains 202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 0.0020 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.115802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089745 restraints weight = 22237.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.092353 restraints weight = 10893.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093293 restraints weight = 7287.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093632 restraints weight = 6611.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093951 restraints weight = 5912.771| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8806 Z= 0.152 Angle : 0.717 10.345 12014 Z= 0.363 Chirality : 0.043 0.238 1383 Planarity : 0.004 0.043 1465 Dihedral : 6.891 58.521 1220 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.26), residues: 1046 helix: 0.48 (0.23), residues: 528 sheet: -3.04 (0.64), residues: 51 loop : -2.42 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.022 0.001 TYR G 44 PHE 0.031 0.002 PHE D 996 TRP 0.019 0.001 TRP D1120 HIS 0.032 0.002 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8801) covalent geometry : angle 0.71046 / 0.36 (12005) hydrogen bonds : bond 0.04424 / 2.81 ( 425) hydrogen bonds : angle 4.94416 / 3.34 ( 1254) metal coordination : bond 0.05085 / 2.54 ( 2) link_NAG-ASN : bond 0.00758 / 0.39 ( 3) link_NAG-ASN : angle 3.60270 / 1.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9243 (m-10) cc_final: 0.8957 (m-10) REVERT: G 139 LEU cc_start: 0.8340 (mm) cc_final: 0.8105 (mm) REVERT: G 141 TYR cc_start: 0.8005 (m-10) cc_final: 0.7731 (m-10) REVERT: G 150 THR cc_start: 0.7867 (t) cc_final: 0.7536 (t) REVERT: G 175 TYR cc_start: 0.6996 (t80) cc_final: 0.6435 (t80) REVERT: G 188 GLU cc_start: 0.8843 (mp0) cc_final: 0.8620 (mp0) REVERT: D 198 MET cc_start: 0.8751 (tmm) cc_final: 0.8295 (tmm) REVERT: D 453 MET cc_start: 0.9030 (tmm) cc_final: 0.8728 (tmm) REVERT: D 460 LYS cc_start: 0.9158 (pttp) cc_final: 0.8853 (pttm) REVERT: D 502 MET cc_start: 0.8283 (tmm) cc_final: 0.7854 (tpp) REVERT: D 530 MET cc_start: 0.9077 (tpp) cc_final: 0.8456 (tpp) REVERT: D 554 PHE cc_start: 0.8239 (t80) cc_final: 0.7648 (t80) REVERT: D 575 PHE cc_start: 0.8855 (m-10) cc_final: 0.8579 (m-10) REVERT: D 579 ASP cc_start: 0.8732 (m-30) cc_final: 0.8517 (m-30) REVERT: D 595 GLU cc_start: 0.8984 (mp0) cc_final: 0.8456 (mp0) REVERT: D 747 LEU cc_start: 0.9104 (mm) cc_final: 0.8891 (mm) REVERT: D 796 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8686 (mp0) REVERT: D 812 LEU cc_start: 0.9293 (pp) cc_final: 0.8544 (pp) REVERT: D 926 GLU cc_start: 0.7999 (pm20) cc_final: 0.7604 (pm20) REVERT: D 966 TRP cc_start: 0.7847 (m100) cc_final: 0.7136 (m100) REVERT: D 1011 TYR cc_start: 0.8884 (m-10) cc_final: 0.8545 (m-80) REVERT: D 1083 MET cc_start: 0.8133 (mmp) cc_final: 0.7882 (mmt) REVERT: D 1126 PHE cc_start: 0.8765 (t80) cc_final: 0.8392 (t80) REVERT: D 1129 CYS cc_start: 0.9061 (t) cc_final: 0.8655 (p) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0713 time to fit residues: 24.7975 Evaluate side-chains 205 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 363 ASN D 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086080 restraints weight = 22445.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088297 restraints weight = 11550.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089111 restraints weight = 8166.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.089376 restraints weight = 7281.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089698 restraints weight = 6663.993| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8806 Z= 0.223 Angle : 0.764 12.081 12014 Z= 0.390 Chirality : 0.044 0.244 1383 Planarity : 0.005 0.049 1465 Dihedral : 7.114 58.001 1220 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.26), residues: 1046 helix: 0.36 (0.22), residues: 528 sheet: -3.04 (0.64), residues: 51 loop : -2.43 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 61 TYR 0.021 0.001 TYR G 44 PHE 0.023 0.002 PHE D 555 TRP 0.015 0.001 TRP D 651 HIS 0.031 0.002 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 ( 8801) covalent geometry : angle 0.75722 / 0.39 (12005) hydrogen bonds : bond 0.04677 / 3.01 ( 425) hydrogen bonds : angle 5.06576 / 3.44 ( 1254) metal coordination : bond 0.05714 / 2.84 ( 2) link_NAG-ASN : bond 0.00706 / 0.37 ( 3) link_NAG-ASN : angle 3.68058 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 PHE cc_start: 0.9254 (t80) cc_final: 0.8987 (t80) REVERT: G 80 TYR cc_start: 0.9236 (m-10) cc_final: 0.8955 (m-10) REVERT: G 98 MET cc_start: 0.8520 (ppp) cc_final: 0.8171 (ppp) REVERT: G 141 TYR cc_start: 0.8100 (m-10) cc_final: 0.7756 (m-10) REVERT: G 150 THR cc_start: 0.7864 (t) cc_final: 0.7508 (t) REVERT: D 198 MET cc_start: 0.8761 (tmm) cc_final: 0.8419 (tmm) REVERT: D 218 ASP cc_start: 0.8610 (m-30) cc_final: 0.8405 (m-30) REVERT: D 287 HIS cc_start: 0.7972 (t-90) cc_final: 0.7708 (t70) REVERT: D 453 MET cc_start: 0.9067 (tmm) cc_final: 0.8719 (tmm) REVERT: D 460 LYS cc_start: 0.9183 (pttp) cc_final: 0.8894 (pttm) REVERT: D 467 ILE cc_start: 0.9169 (mp) cc_final: 0.8890 (mp) REVERT: D 502 MET cc_start: 0.8318 (tmm) cc_final: 0.7881 (tpp) REVERT: D 530 MET cc_start: 0.9075 (tpp) cc_final: 0.8327 (tpp) REVERT: D 533 PHE cc_start: 0.9035 (t80) cc_final: 0.8778 (t80) REVERT: D 554 PHE cc_start: 0.8084 (t80) cc_final: 0.7498 (t80) REVERT: D 575 PHE cc_start: 0.8859 (m-10) cc_final: 0.8561 (m-10) REVERT: D 579 ASP cc_start: 0.8760 (m-30) cc_final: 0.8528 (m-30) REVERT: D 595 GLU cc_start: 0.8995 (mp0) cc_final: 0.8460 (mp0) REVERT: D 648 MET cc_start: 0.9239 (tpt) cc_final: 0.8989 (tpp) REVERT: D 796 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8786 (mp0) REVERT: D 812 LEU cc_start: 0.9328 (pp) cc_final: 0.8664 (pp) REVERT: D 926 GLU cc_start: 0.8086 (pm20) cc_final: 0.7676 (pm20) REVERT: D 1011 TYR cc_start: 0.9115 (m-10) cc_final: 0.8703 (m-80) REVERT: D 1126 PHE cc_start: 0.8932 (t80) cc_final: 0.8495 (t80) REVERT: D 1129 CYS cc_start: 0.9040 (t) cc_final: 0.8793 (p) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0711 time to fit residues: 23.9301 Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 0.0170 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 0.0370 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 363 ASN D 493 HIS D 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091097 restraints weight = 22263.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.093626 restraints weight = 10812.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094457 restraints weight = 7421.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094788 restraints weight = 6762.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095027 restraints weight = 6064.142| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8806 Z= 0.150 Angle : 0.757 12.158 12014 Z= 0.380 Chirality : 0.043 0.240 1383 Planarity : 0.005 0.063 1465 Dihedral : 7.006 59.624 1220 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.26), residues: 1046 helix: 0.55 (0.22), residues: 524 sheet: -2.95 (0.65), residues: 49 loop : -2.36 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 61 TYR 0.019 0.001 TYR D 468 PHE 0.015 0.002 PHE D 830 TRP 0.016 0.001 TRP D1120 HIS 0.026 0.002 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8801) covalent geometry : angle 0.75124 / 0.38 (12005) hydrogen bonds : bond 0.04412 / 2.81 ( 425) hydrogen bonds : angle 4.95424 / 3.36 ( 1254) metal coordination : bond 0.04181 / 2.08 ( 2) link_NAG-ASN : bond 0.00757 / 0.39 ( 3) link_NAG-ASN : angle 3.62103 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9173 (m-10) cc_final: 0.8914 (m-10) REVERT: G 98 MET cc_start: 0.8764 (ppp) cc_final: 0.8369 (ppp) REVERT: G 150 THR cc_start: 0.7845 (t) cc_final: 0.7477 (t) REVERT: G 175 TYR cc_start: 0.6932 (t80) cc_final: 0.6553 (t80) REVERT: D 198 MET cc_start: 0.8699 (tmm) cc_final: 0.8287 (tmm) REVERT: D 287 HIS cc_start: 0.7795 (t-90) cc_final: 0.7536 (t-90) REVERT: D 401 MET cc_start: 0.7350 (ptp) cc_final: 0.6978 (pmm) REVERT: D 453 MET cc_start: 0.9058 (tmm) cc_final: 0.8757 (tmm) REVERT: D 460 LYS cc_start: 0.9127 (pttp) cc_final: 0.8799 (pttm) REVERT: D 502 MET cc_start: 0.8277 (tmm) cc_final: 0.7846 (tpp) REVERT: D 530 MET cc_start: 0.9063 (tpp) cc_final: 0.8386 (tpp) REVERT: D 554 PHE cc_start: 0.7635 (t80) cc_final: 0.7322 (t80) REVERT: D 575 PHE cc_start: 0.8863 (m-10) cc_final: 0.8214 (m-80) REVERT: D 579 ASP cc_start: 0.8750 (m-30) cc_final: 0.8496 (m-30) REVERT: D 595 GLU cc_start: 0.8969 (mp0) cc_final: 0.8397 (mp0) REVERT: D 648 MET cc_start: 0.9208 (tpt) cc_final: 0.8931 (tpp) REVERT: D 747 LEU cc_start: 0.9166 (mm) cc_final: 0.8951 (mm) REVERT: D 796 GLU cc_start: 0.8954 (mt-10) cc_final: 0.7875 (tm-30) REVERT: D 926 GLU cc_start: 0.7949 (pm20) cc_final: 0.7545 (pm20) REVERT: D 966 TRP cc_start: 0.7847 (m100) cc_final: 0.7238 (m100) REVERT: D 1011 TYR cc_start: 0.9077 (m-10) cc_final: 0.8673 (m-80) REVERT: D 1126 PHE cc_start: 0.8913 (t80) cc_final: 0.8494 (t80) REVERT: D 1129 CYS cc_start: 0.8902 (t) cc_final: 0.8669 (p) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.0631 time to fit residues: 21.2044 Evaluate side-chains 199 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089496 restraints weight = 21913.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092298 restraints weight = 12446.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094092 restraints weight = 8550.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.095317 restraints weight = 6700.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096054 restraints weight = 5681.181| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8806 Z= 0.144 Angle : 0.738 11.732 12014 Z= 0.368 Chirality : 0.042 0.245 1383 Planarity : 0.004 0.051 1465 Dihedral : 6.872 58.165 1220 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.26), residues: 1046 helix: 0.60 (0.23), residues: 525 sheet: -2.85 (0.66), residues: 48 loop : -2.33 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 61 TYR 0.013 0.001 TYR D 499 PHE 0.018 0.002 PHE G 73 TRP 0.014 0.001 TRP D 651 HIS 0.028 0.002 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8801) covalent geometry : angle 0.73243 / 0.37 (12005) hydrogen bonds : bond 0.04256 / 2.71 ( 425) hydrogen bonds : angle 4.88455 / 3.33 ( 1254) metal coordination : bond 0.05392 / 2.69 ( 2) link_NAG-ASN : bond 0.00764 / 0.40 ( 3) link_NAG-ASN : angle 3.47918 / 1.56 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 80 TYR cc_start: 0.9173 (m-10) cc_final: 0.8843 (m-10) REVERT: G 98 MET cc_start: 0.8748 (ppp) cc_final: 0.8428 (ppp) REVERT: G 150 THR cc_start: 0.7809 (t) cc_final: 0.7428 (t) REVERT: D 198 MET cc_start: 0.8783 (tmm) cc_final: 0.8333 (tmm) REVERT: D 287 HIS cc_start: 0.7805 (t-90) cc_final: 0.7581 (t70) REVERT: D 401 MET cc_start: 0.7268 (ptp) cc_final: 0.6893 (pmm) REVERT: D 460 LYS cc_start: 0.9144 (pttp) cc_final: 0.8778 (pttm) REVERT: D 467 ILE cc_start: 0.9108 (mp) cc_final: 0.8901 (mp) REVERT: D 502 MET cc_start: 0.8217 (tmm) cc_final: 0.7785 (tpp) REVERT: D 530 MET cc_start: 0.9034 (tpp) cc_final: 0.8673 (tpp) REVERT: D 554 PHE cc_start: 0.7848 (t80) cc_final: 0.7521 (t80) REVERT: D 559 ASN cc_start: 0.8444 (m110) cc_final: 0.8100 (m110) REVERT: D 575 PHE cc_start: 0.8910 (m-10) cc_final: 0.8597 (m-10) REVERT: D 579 ASP cc_start: 0.8752 (m-30) cc_final: 0.8519 (m-30) REVERT: D 595 GLU cc_start: 0.8971 (mp0) cc_final: 0.8387 (mp0) REVERT: D 648 MET cc_start: 0.9183 (tpt) cc_final: 0.8933 (tpp) REVERT: D 747 LEU cc_start: 0.9127 (mm) cc_final: 0.8915 (mm) REVERT: D 767 GLU cc_start: 0.8742 (mp0) cc_final: 0.8230 (mp0) REVERT: D 796 GLU cc_start: 0.8895 (mt-10) cc_final: 0.7880 (tm-30) REVERT: D 926 GLU cc_start: 0.7890 (pm20) cc_final: 0.7512 (pm20) REVERT: D 966 TRP cc_start: 0.7739 (m100) cc_final: 0.7157 (m100) REVERT: D 986 ILE cc_start: 0.9144 (tp) cc_final: 0.8928 (tp) REVERT: D 1011 TYR cc_start: 0.9050 (m-10) cc_final: 0.8638 (m-80) REVERT: D 1085 MET cc_start: 0.8657 (tpp) cc_final: 0.7887 (tpp) REVERT: D 1126 PHE cc_start: 0.8874 (t80) cc_final: 0.8592 (t80) REVERT: D 1129 CYS cc_start: 0.8887 (t) cc_final: 0.8618 (p) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0665 time to fit residues: 23.5291 Evaluate side-chains 204 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN D 363 ASN D 572 ASN D 779 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086291 restraints weight = 22520.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088439 restraints weight = 11265.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089741 restraints weight = 8076.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089946 restraints weight = 7072.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090221 restraints weight = 6241.350| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 8806 Z= 0.250 Angle : 0.816 11.336 12014 Z= 0.410 Chirality : 0.046 0.248 1383 Planarity : 0.005 0.043 1465 Dihedral : 7.266 57.067 1220 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.26), residues: 1046 helix: 0.36 (0.22), residues: 527 sheet: -3.18 (0.63), residues: 51 loop : -2.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 61 TYR 0.024 0.002 TYR D 499 PHE 0.040 0.002 PHE D 996 TRP 0.016 0.001 TRP D 651 HIS 0.028 0.002 HIS G 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 ( 8801) covalent geometry : angle 0.80994 / 0.41 (12005) hydrogen bonds : bond 0.04762 / 3.04 ( 425) hydrogen bonds : angle 5.12059 / 3.50 ( 1254) metal coordination : bond 0.05764 / 2.87 ( 2) link_NAG-ASN : bond 0.00716 / 0.37 ( 3) link_NAG-ASN : angle 3.61941 / 1.63 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.80 seconds wall clock time: 23 minutes 13.89 seconds (1393.89 seconds total)