Starting phenix.real_space_refine on Thu Mar 5 00:45:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.map" model { file = "/net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7m_20266/03_2026/6p7m_20266.cif" } resolution = 3.0 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= 0.071 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 8946 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: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 6417 2.51 5 N 1673 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10141 At special positions: 0 Unit cell: (100.8, 114.3, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 25 15.00 Mg 2 11.99 O 1996 8.00 N 1673 7.00 C 6417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 491.1 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.2% alpha, 12.6% beta 6 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 38 through 66 removed outlier: 4.573A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.616A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.209A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.544A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.904A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.598A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.451A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.648A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.966A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.479A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 718 through 728 removed outlier: 4.077A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.101A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 890 through 919 removed outlier: 4.005A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 969 through 973 removed outlier: 4.296A pdb=" N GLY A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.255A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.793A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'C' and resid 137 through 148 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.533A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 229 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.794A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.794A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 784 removed outlier: 3.764A pdb=" N GLU C 184 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 784 removed outlier: 4.158A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 222 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 855 removed outlier: 6.410A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.509A pdb=" N LEU A1065 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1073 455 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2510 1.33 - 1.45: 2118 1.45 - 1.57: 5668 1.57 - 1.69: 50 1.69 - 1.81: 47 Bond restraints: 10393 Sorted by residual: bond pdb=" CB VAL A 921 " pdb=" CG1 VAL A 921 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB ILE A 802 " pdb=" CG2 ILE A 802 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" C VAL A 921 " pdb=" N ILE A 922 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.73e-02 3.34e+03 1.45e+00 bond pdb=" C ILE A 829 " pdb=" N GLY A 830 " ideal model delta sigma weight residual 1.332 1.324 0.008 6.60e-03 2.30e+04 1.36e+00 bond pdb=" CB VAL A 757 " pdb=" CG2 VAL A 757 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 ... (remaining 10388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13572 1.41 - 2.82: 439 2.82 - 4.22: 72 4.22 - 5.63: 14 5.63 - 7.04: 6 Bond angle restraints: 14103 Sorted by residual: angle pdb=" C SER A 987 " pdb=" N THR A 988 " pdb=" CA THR A 988 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C2' C B 9 " pdb=" C1' C B 9 " pdb=" N1 C B 9 " ideal model delta sigma weight residual 112.00 115.88 -3.88 1.50e+00 4.44e-01 6.68e+00 angle pdb=" C LEU A 497 " pdb=" N LEU A 498 " pdb=" CA LEU A 498 " ideal model delta sigma weight residual 122.31 117.20 5.11 2.00e+00 2.50e-01 6.53e+00 angle pdb=" N THR A 988 " pdb=" CA THR A 988 " pdb=" C THR A 988 " ideal model delta sigma weight residual 110.80 115.87 -5.07 2.13e+00 2.20e-01 5.67e+00 angle pdb=" C GLU A 354 " pdb=" N TRP A 355 " pdb=" CA TRP A 355 " ideal model delta sigma weight residual 121.19 124.96 -3.77 1.59e+00 3.96e-01 5.61e+00 ... (remaining 14098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.22: 6104 31.22 - 62.44: 182 62.44 - 93.66: 19 93.66 - 124.89: 0 124.89 - 156.11: 1 Dihedral angle restraints: 6306 sinusoidal: 2845 harmonic: 3461 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.89 156.11 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" CA ALA A 195 " pdb=" C ALA A 195 " pdb=" N ILE A 196 " pdb=" CA ILE A 196 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN A1170 " pdb=" C GLN A1170 " pdb=" N GLU A1171 " pdb=" CA GLU A1171 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 6303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1015 0.041 - 0.082: 408 0.082 - 0.122: 97 0.122 - 0.163: 20 0.163 - 0.204: 1 Chirality restraints: 1541 Sorted by residual: chirality pdb=" C1' C B 9 " pdb=" O4' C B 9 " pdb=" C2' C B 9 " pdb=" N1 C B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' U B 4 " pdb=" O4' U B 4 " pdb=" C2' U B 4 " pdb=" N1 U B 4 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1538 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 9 " -0.023 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C B 9 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C B 9 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B 9 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C B 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 9 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C B 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C B 9 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 129 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 5 " -0.019 2.00e-02 2.50e+03 9.93e-03 2.22e+00 pdb=" N1 U B 5 " 0.021 2.00e-02 2.50e+03 pdb=" C2 U B 5 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U B 5 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U B 5 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U B 5 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 5 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 5 " 0.004 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 116 2.61 - 3.19: 9062 3.19 - 3.76: 15101 3.76 - 4.33: 22524 4.33 - 4.90: 36716 Nonbonded interactions: 83519 Sorted by model distance: nonbonded pdb=" OP2 A B 17 " pdb="MG MG B 101 " model vdw 2.043 2.170 nonbonded pdb=" OD1 ASP A 367 " pdb=" OH TYR A 381 " model vdw 2.105 3.040 nonbonded pdb=" O TYR A1049 " pdb=" OG1 THR A1055 " model vdw 2.138 3.040 nonbonded pdb=" NZ LYS A 206 " pdb=" O LYS A 253 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASP A 297 " pdb=" OH TYR A 510 " model vdw 2.181 3.040 ... (remaining 83514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.110 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10393 Z= 0.258 Angle : 0.627 7.037 14103 Z= 0.349 Chirality : 0.045 0.204 1541 Planarity : 0.003 0.041 1709 Dihedral : 14.905 156.108 4072 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1150 helix: -1.49 (0.20), residues: 515 sheet: -2.84 (0.37), residues: 143 loop : -2.78 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1189 TYR 0.025 0.002 TYR A 840 PHE 0.017 0.002 PHE A 328 TRP 0.011 0.001 TRP A 355 HIS 0.010 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00598 (10393) covalent geometry : angle 0.62714 (14103) hydrogen bonds : bond 0.13930 ( 443) hydrogen bonds : angle 6.47703 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.7868 (mt0) cc_final: 0.7261 (pt0) REVERT: A 858 GLU cc_start: 0.8357 (pt0) cc_final: 0.8153 (pt0) REVERT: A 1128 MET cc_start: 0.8630 (mmm) cc_final: 0.8187 (mmm) REVERT: C 230 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7250 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5847 time to fit residues: 84.6606 Evaluate side-chains 94 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 157 ASN A 268 GLN A 420 GLN A 793 GLN A 864 ASN A 909 HIS A 955 ASN C 168 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096410 restraints weight = 14861.309| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.37 r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10393 Z= 0.135 Angle : 0.537 7.164 14103 Z= 0.286 Chirality : 0.042 0.176 1541 Planarity : 0.003 0.033 1709 Dihedral : 11.545 163.966 1636 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.80 % Allowed : 9.86 % Favored : 88.34 % 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: -1.85 (0.24), residues: 1150 helix: -0.15 (0.23), residues: 521 sheet: -2.39 (0.40), residues: 135 loop : -2.02 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 217 TYR 0.009 0.001 TYR A 794 PHE 0.010 0.001 PHE A 220 TRP 0.008 0.001 TRP A1193 HIS 0.004 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00304 (10393) covalent geometry : angle 0.53707 (14103) hydrogen bonds : bond 0.04181 ( 443) hydrogen bonds : angle 4.80874 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 VAL cc_start: 0.8146 (t) cc_final: 0.7882 (p) REVERT: A 264 GLN cc_start: 0.7815 (mt0) cc_final: 0.6988 (pt0) REVERT: A 746 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.7811 (tmt) REVERT: A 819 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7882 (mm) REVERT: A 941 GLN cc_start: 0.8356 (mp10) cc_final: 0.8051 (mp10) REVERT: C 227 GLU cc_start: 0.8477 (tp30) cc_final: 0.8070 (tp30) REVERT: C 230 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7229 (mtm-85) outliers start: 19 outliers final: 4 residues processed: 127 average time/residue: 0.5333 time to fit residues: 73.2803 Evaluate side-chains 102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 864 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090678 restraints weight = 15045.901| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.34 r_work: 0.3037 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10393 Z= 0.325 Angle : 0.651 7.890 14103 Z= 0.344 Chirality : 0.048 0.204 1541 Planarity : 0.004 0.034 1709 Dihedral : 11.523 156.167 1636 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.22 % Allowed : 12.42 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1150 helix: -0.02 (0.23), residues: 520 sheet: -2.47 (0.38), residues: 147 loop : -1.90 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 217 TYR 0.021 0.002 TYR A 262 PHE 0.018 0.002 PHE A 328 TRP 0.009 0.001 TRP A 355 HIS 0.010 0.002 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00767 (10393) covalent geometry : angle 0.65145 (14103) hydrogen bonds : bond 0.05083 ( 443) hydrogen bonds : angle 5.01613 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7933 (p) REVERT: A 264 GLN cc_start: 0.7880 (mt0) cc_final: 0.7056 (pt0) REVERT: A 746 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.7876 (tmt) REVERT: A 819 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7933 (mm) REVERT: A 1035 MET cc_start: 0.8413 (ptm) cc_final: 0.8071 (ptm) REVERT: A 1073 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7581 (ptt90) REVERT: C 227 GLU cc_start: 0.8842 (tp30) cc_final: 0.8410 (tp30) REVERT: C 230 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7270 (mtm-85) outliers start: 34 outliers final: 17 residues processed: 114 average time/residue: 0.4884 time to fit residues: 60.8060 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096042 restraints weight = 14938.242| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.35 r_work: 0.3117 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10393 Z= 0.124 Angle : 0.507 7.573 14103 Z= 0.270 Chirality : 0.041 0.172 1541 Planarity : 0.003 0.031 1709 Dihedral : 11.458 164.705 1636 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.56 % Allowed : 15.55 % Favored : 81.90 % 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: -1.07 (0.25), residues: 1150 helix: 0.52 (0.24), residues: 521 sheet: -2.28 (0.38), residues: 149 loop : -1.51 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 217 TYR 0.018 0.001 TYR A 262 PHE 0.009 0.001 PHE A 486 TRP 0.008 0.001 TRP A1193 HIS 0.004 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00280 (10393) covalent geometry : angle 0.50739 (14103) hydrogen bonds : bond 0.03826 ( 443) hydrogen bonds : angle 4.48965 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.7824 (mt0) cc_final: 0.7043 (pt0) REVERT: A 746 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.7867 (tmt) REVERT: A 819 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7892 (mm) REVERT: A 941 GLN cc_start: 0.8371 (mp10) cc_final: 0.8039 (mp10) REVERT: A 1035 MET cc_start: 0.8313 (ptm) cc_final: 0.7920 (ptm) REVERT: A 1065 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7989 (pp) REVERT: C 202 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7981 (tppp) REVERT: C 227 GLU cc_start: 0.8865 (tp30) cc_final: 0.8471 (tp30) REVERT: C 230 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7366 (mtm-85) outliers start: 27 outliers final: 11 residues processed: 119 average time/residue: 0.4935 time to fit residues: 63.9322 Evaluate side-chains 105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 864 ASN A 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090211 restraints weight = 15157.802| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.35 r_work: 0.3027 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10393 Z= 0.345 Angle : 0.657 7.714 14103 Z= 0.347 Chirality : 0.049 0.208 1541 Planarity : 0.004 0.033 1709 Dihedral : 11.497 155.940 1636 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.03 % Allowed : 16.30 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1150 helix: 0.38 (0.24), residues: 509 sheet: -2.32 (0.38), residues: 147 loop : -1.47 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 217 TYR 0.017 0.002 TYR A 794 PHE 0.018 0.002 PHE A 702 TRP 0.010 0.001 TRP A 355 HIS 0.009 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00813 (10393) covalent geometry : angle 0.65651 (14103) hydrogen bonds : bond 0.05079 ( 443) hydrogen bonds : angle 4.88698 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 GLN cc_start: 0.7902 (mt0) cc_final: 0.7089 (pt0) REVERT: A 746 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.7867 (tmt) REVERT: A 819 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 858 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: A 1035 MET cc_start: 0.8393 (ptm) cc_final: 0.7985 (ptm) REVERT: A 1073 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7586 (ptt90) REVERT: A 1137 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: C 227 GLU cc_start: 0.9027 (tp30) cc_final: 0.8726 (tp30) REVERT: C 230 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7312 (mtm-85) outliers start: 32 outliers final: 18 residues processed: 116 average time/residue: 0.5114 time to fit residues: 64.4761 Evaluate side-chains 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 975 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.094933 restraints weight = 15015.236| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.34 r_work: 0.3096 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10393 Z= 0.141 Angle : 0.518 8.554 14103 Z= 0.275 Chirality : 0.042 0.177 1541 Planarity : 0.003 0.033 1709 Dihedral : 11.451 163.240 1636 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.13 % Allowed : 17.25 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1150 helix: 0.75 (0.24), residues: 516 sheet: -2.24 (0.39), residues: 147 loop : -1.23 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 217 TYR 0.019 0.001 TYR A 262 PHE 0.010 0.001 PHE A 702 TRP 0.008 0.001 TRP A1193 HIS 0.004 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00323 (10393) covalent geometry : angle 0.51845 (14103) hydrogen bonds : bond 0.03956 ( 443) hydrogen bonds : angle 4.47884 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7023 (mtm180) REVERT: A 264 GLN cc_start: 0.7800 (mt0) cc_final: 0.7046 (pt0) REVERT: A 435 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 746 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.7875 (tmt) REVERT: A 819 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 941 GLN cc_start: 0.8356 (mp10) cc_final: 0.8059 (mp10) REVERT: A 1035 MET cc_start: 0.8371 (ptm) cc_final: 0.8026 (ptm) REVERT: A 1065 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8149 (pp) REVERT: A 1073 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7586 (ptt90) REVERT: C 202 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7986 (tppp) REVERT: C 227 GLU cc_start: 0.9014 (tp30) cc_final: 0.8723 (tp30) REVERT: C 230 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7352 (mtm-85) outliers start: 33 outliers final: 15 residues processed: 118 average time/residue: 0.4719 time to fit residues: 60.8702 Evaluate side-chains 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 975 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093255 restraints weight = 15021.165| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.35 r_work: 0.3074 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10393 Z= 0.215 Angle : 0.562 7.924 14103 Z= 0.297 Chirality : 0.044 0.190 1541 Planarity : 0.003 0.032 1709 Dihedral : 11.425 161.150 1636 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.65 % Allowed : 18.39 % Favored : 78.96 % 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: -0.75 (0.25), residues: 1150 helix: 0.74 (0.24), residues: 516 sheet: -2.22 (0.39), residues: 147 loop : -1.21 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.014 0.001 TYR A 262 PHE 0.013 0.001 PHE A 702 TRP 0.008 0.001 TRP A 355 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00505 (10393) covalent geometry : angle 0.56205 (14103) hydrogen bonds : bond 0.04325 ( 443) hydrogen bonds : angle 4.57366 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7051 (mtm180) REVERT: A 227 PHE cc_start: 0.7522 (t80) cc_final: 0.7240 (t80) REVERT: A 264 GLN cc_start: 0.7825 (mt0) cc_final: 0.7004 (pt0) REVERT: A 305 ARG cc_start: 0.6995 (mtp-110) cc_final: 0.6614 (mtp85) REVERT: A 435 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 746 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.7896 (tmt) REVERT: A 819 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7891 (mm) REVERT: A 858 GLU cc_start: 0.8987 (pt0) cc_final: 0.8356 (mt-10) REVERT: A 941 GLN cc_start: 0.8358 (mp10) cc_final: 0.8038 (mp10) REVERT: A 949 MET cc_start: 0.8651 (mtp) cc_final: 0.8390 (mtp) REVERT: A 1065 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 1073 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7622 (ptt90) REVERT: C 227 GLU cc_start: 0.9027 (tp30) cc_final: 0.8717 (tp30) REVERT: C 230 ARG cc_start: 0.7651 (ttm170) cc_final: 0.7321 (mtm-85) outliers start: 28 outliers final: 19 residues processed: 113 average time/residue: 0.4735 time to fit residues: 58.1204 Evaluate side-chains 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN A 975 GLN C 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094327 restraints weight = 14940.152| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.34 r_work: 0.3094 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10393 Z= 0.176 Angle : 0.536 8.415 14103 Z= 0.283 Chirality : 0.043 0.182 1541 Planarity : 0.003 0.042 1709 Dihedral : 11.419 162.889 1636 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.75 % Allowed : 18.96 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1150 helix: 0.84 (0.24), residues: 516 sheet: -2.17 (0.39), residues: 147 loop : -1.13 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.023 0.001 TYR A 262 PHE 0.010 0.001 PHE A 702 TRP 0.009 0.001 TRP A 999 HIS 0.004 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00411 (10393) covalent geometry : angle 0.53558 (14103) hydrogen bonds : bond 0.04078 ( 443) hydrogen bonds : angle 4.48147 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7052 (mtm180) REVERT: A 227 PHE cc_start: 0.7472 (t80) cc_final: 0.7076 (t80) REVERT: A 264 GLN cc_start: 0.7849 (mt0) cc_final: 0.7128 (pt0) REVERT: A 305 ARG cc_start: 0.6984 (mtp-110) cc_final: 0.6605 (mtp85) REVERT: A 435 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8772 (mm) REVERT: A 526 GLN cc_start: 0.8512 (mp10) cc_final: 0.8267 (pm20) REVERT: A 746 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.7888 (tmt) REVERT: A 819 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7855 (mm) REVERT: A 858 GLU cc_start: 0.8956 (pt0) cc_final: 0.8329 (mt-10) REVERT: A 941 GLN cc_start: 0.8347 (mp10) cc_final: 0.8035 (mp10) REVERT: A 949 MET cc_start: 0.8633 (mtp) cc_final: 0.8362 (mtp) REVERT: A 1035 MET cc_start: 0.8359 (ptm) cc_final: 0.8021 (ptm) REVERT: A 1065 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8201 (pp) REVERT: A 1073 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7627 (ptt90) REVERT: C 202 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.7963 (tppp) REVERT: C 227 GLU cc_start: 0.9069 (tp30) cc_final: 0.8852 (tp30) REVERT: C 230 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7326 (mtm-85) outliers start: 29 outliers final: 17 residues processed: 113 average time/residue: 0.4961 time to fit residues: 61.0881 Evaluate side-chains 121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095369 restraints weight = 14818.450| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.30 r_work: 0.3104 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10393 Z= 0.149 Angle : 0.520 9.833 14103 Z= 0.275 Chirality : 0.042 0.175 1541 Planarity : 0.003 0.035 1709 Dihedral : 11.397 164.452 1636 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 19.05 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.26), residues: 1150 helix: 0.97 (0.24), residues: 516 sheet: -2.10 (0.39), residues: 147 loop : -1.03 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.013 0.001 TYR A 262 PHE 0.009 0.001 PHE A 61 TRP 0.008 0.001 TRP A 999 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00347 (10393) covalent geometry : angle 0.51989 (14103) hydrogen bonds : bond 0.03879 ( 443) hydrogen bonds : angle 4.39437 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7047 (mtm110) REVERT: A 64 ASP cc_start: 0.8102 (t0) cc_final: 0.7048 (m-30) REVERT: A 227 PHE cc_start: 0.7454 (t80) cc_final: 0.7129 (t80) REVERT: A 264 GLN cc_start: 0.7792 (mt0) cc_final: 0.7030 (pt0) REVERT: A 305 ARG cc_start: 0.6968 (mtp-110) cc_final: 0.6608 (mtp85) REVERT: A 435 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 526 GLN cc_start: 0.8518 (mp10) cc_final: 0.8293 (pm20) REVERT: A 746 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.7870 (tmt) REVERT: A 819 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7861 (mm) REVERT: A 858 GLU cc_start: 0.8955 (pt0) cc_final: 0.8328 (mt-10) REVERT: A 941 GLN cc_start: 0.8354 (mp10) cc_final: 0.8044 (mp10) REVERT: A 949 MET cc_start: 0.8611 (mtp) cc_final: 0.8339 (mtp) REVERT: A 1035 MET cc_start: 0.8316 (ptm) cc_final: 0.8049 (ptm) REVERT: A 1065 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8158 (pp) REVERT: A 1073 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7573 (ptt90) REVERT: C 202 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7980 (tppp) REVERT: C 217 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7213 (mtp-110) REVERT: C 227 GLU cc_start: 0.9074 (tp30) cc_final: 0.8867 (tp30) REVERT: C 230 ARG cc_start: 0.7652 (ttm170) cc_final: 0.7369 (mtm-85) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 0.4747 time to fit residues: 60.1407 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096511 restraints weight = 14658.512| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.32 r_work: 0.3124 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10393 Z= 0.130 Angle : 0.518 9.428 14103 Z= 0.273 Chirality : 0.042 0.167 1541 Planarity : 0.003 0.036 1709 Dihedral : 11.356 165.968 1636 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.27 % Allowed : 19.81 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1150 helix: 1.13 (0.24), residues: 515 sheet: -1.93 (0.39), residues: 149 loop : -0.92 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.018 0.001 TYR A 262 PHE 0.009 0.001 PHE A 61 TRP 0.010 0.001 TRP A 999 HIS 0.003 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00299 (10393) covalent geometry : angle 0.51763 (14103) hydrogen bonds : bond 0.03694 ( 443) hydrogen bonds : angle 4.30929 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8198 (t0) cc_final: 0.7198 (m-30) REVERT: A 227 PHE cc_start: 0.7375 (t80) cc_final: 0.6963 (t80) REVERT: A 236 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 264 GLN cc_start: 0.7828 (mt0) cc_final: 0.7119 (pt0) REVERT: A 305 ARG cc_start: 0.6973 (mtp-110) cc_final: 0.6626 (mtp85) REVERT: A 435 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8806 (mm) REVERT: A 526 GLN cc_start: 0.8556 (mp10) cc_final: 0.8269 (pm20) REVERT: A 746 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.7866 (tmt) REVERT: A 819 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7860 (mm) REVERT: A 858 GLU cc_start: 0.8952 (pt0) cc_final: 0.8345 (mt-10) REVERT: A 941 GLN cc_start: 0.8368 (mp10) cc_final: 0.8060 (mp10) REVERT: A 949 MET cc_start: 0.8614 (mtp) cc_final: 0.8343 (mtp) REVERT: A 1035 MET cc_start: 0.8295 (ptm) cc_final: 0.8023 (ptm) REVERT: A 1065 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8133 (pp) REVERT: A 1073 ARG cc_start: 0.8255 (ptm160) cc_final: 0.7601 (ptt90) REVERT: A 1204 GLU cc_start: 0.8693 (mp0) cc_final: 0.8336 (mm-30) REVERT: C 202 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7987 (tppp) REVERT: C 217 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7075 (mtp180) REVERT: C 230 ARG cc_start: 0.7730 (ttm170) cc_final: 0.7427 (mtm-85) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.4656 time to fit residues: 58.1884 Evaluate side-chains 116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097249 restraints weight = 14808.205| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.31 r_work: 0.3135 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10393 Z= 0.122 Angle : 0.516 11.091 14103 Z= 0.269 Chirality : 0.041 0.164 1541 Planarity : 0.003 0.036 1709 Dihedral : 11.331 166.650 1636 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.09 % Allowed : 19.81 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1150 helix: 1.23 (0.24), residues: 517 sheet: -1.84 (0.40), residues: 149 loop : -0.80 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.010 0.001 TYR C 139 PHE 0.009 0.001 PHE A 109 TRP 0.010 0.001 TRP A 999 HIS 0.003 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00280 (10393) covalent geometry : angle 0.51580 (14103) hydrogen bonds : bond 0.03588 ( 443) hydrogen bonds : angle 4.22719 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3238.24 seconds wall clock time: 55 minutes 52.31 seconds (3352.31 seconds total)