Starting phenix.real_space_refine on Sat Sep 12 19:02:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7m_20266/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_2026/6p7m_20266.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p7m_20266/09_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-2.2.1-6174/lib/python3.11/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, 'RNAv2': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 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: 2.08, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 601.3 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: 1.57 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: 2.49 Time building geometry restraints manager: 1.34 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: 13464 1.41 - 2.82: 482 2.82 - 4.22: 115 4.22 - 5.63: 33 5.63 - 7.04: 6 Bond angle restraints: 14100 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=" O3' A B 21 " pdb=" C3' A B 21 " pdb=" C2' A B 21 " ideal model delta sigma weight residual 113.80 108.49 5.31 2.00e+00 2.50e-01 7.04e+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=" O3' A B 2 " pdb=" C3' A B 2 " pdb=" C2' A B 2 " ideal model delta sigma weight residual 113.80 108.88 4.92 2.00e+00 2.50e-01 6.04e+00 angle pdb=" C3' A B 12 " pdb=" C2' A B 12 " pdb=" O2' A B 12 " ideal model delta sigma weight residual 109.80 114.57 -4.77 2.00e+00 2.50e-01 5.69e+00 ... (remaining 14095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 5362 15.78 - 31.56: 661 31.56 - 47.35: 135 47.35 - 63.13: 60 63.13 - 78.91: 19 Dihedral angle restraints: 6237 sinusoidal: 2776 harmonic: 3461 Sorted by residual: dihedral pdb=" C4' U B 10 " pdb=" C3' U B 10 " pdb=" C2' U B 10 " pdb=" C1' U B 10 " ideal model delta sinusoidal sigma weight residual 36.35 -37.21 73.55 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' A B 11 " pdb=" C3' A B 11 " pdb=" C2' A B 11 " pdb=" C1' A B 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.80 73.14 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' U B 14 " pdb=" C3' U B 14 " pdb=" C2' U B 14 " pdb=" C1' U B 14 " ideal model delta sinusoidal sigma weight residual 36.34 -36.40 72.74 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1237 0.060 - 0.120: 237 0.120 - 0.180: 28 0.180 - 0.240: 26 0.240 - 0.300: 13 Chirality restraints: 1541 Sorted by residual: chirality pdb=" C2' A B 11 " pdb=" C3' A B 11 " pdb=" O2' A B 11 " pdb=" C1' A B 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' U B 10 " pdb=" C3' U B 10 " pdb=" O2' U B 10 " pdb=" C1' U B 10 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2' A B 1 " pdb=" C3' A B 1 " pdb=" O2' A B 1 " pdb=" C1' A B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (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: 3.880 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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= 0.259 Angle : 0.688 7.037 14100 Z= 0.364 Chirality : 0.059 0.300 1541 Planarity : 0.003 0.041 1709 Dihedral : 15.377 78.911 4003 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/Z covalent geometry : bond 0.00602 / 0.26 (10393) covalent geometry : angle 0.68803 / 0.36 (14100) hydrogen bonds : bond 0.13930 / 9.30 ( 443) hydrogen bonds : angle 6.47703 / 4.57 ( 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 : 0.290 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: 0.5557 time to fit residues: 80.9132 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 : 0.398 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.6980 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.124855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097140 restraints weight = 14777.476| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.31 r_work: 0.3140 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1263 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= 0.158 Angle : 0.700 13.449 14100 Z= 0.336 Chirality : 0.066 0.886 1541 Planarity : 0.004 0.033 1709 Dihedral : 11.436 147.126 1567 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.99 % Allowed : 10.05 % Favored : 87.96 % 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: -1.91 (0.24), residues: 1150 helix: -0.20 (0.23), residues: 520 sheet: -2.39 (0.40), residues: 135 loop : -2.05 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 217 TYR 0.010 0.001 TYR A 794 PHE 0.010 0.001 PHE A 227 TRP 0.007 0.001 TRP A1193 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10393) covalent geometry : angle 0.70012 / 0.34 (14100) hydrogen bonds : bond 0.04505 / 2.92 ( 443) hydrogen bonds : angle 4.89031 / 3.43 ( 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 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 264 GLN cc_start: 0.7827 (mt0) cc_final: 0.6995 (pt0) REVERT: A 746 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.7828 (tmt) REVERT: A 819 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7895 (mm) REVERT: C 227 GLU cc_start: 0.8418 (tp30) cc_final: 0.8016 (tp30) REVERT: C 230 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7204 (mtm-85) outliers start: 21 outliers final: 6 residues processed: 124 average time/residue: 0.4986 time to fit residues: 67.3416 Evaluate side-chains 104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 431 SER 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: 5.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 864 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093071 restraints weight = 14998.186| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.31 r_work: 0.3073 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10393 Z= 0.285 Angle : 0.738 10.011 14100 Z= 0.363 Chirality : 0.066 0.673 1541 Planarity : 0.004 0.033 1709 Dihedral : 11.265 142.862 1567 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.03 % Allowed : 12.32 % Favored : 84.64 % 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: -1.68 (0.24), residues: 1150 helix: 0.01 (0.23), residues: 520 sheet: -2.45 (0.38), residues: 147 loop : -1.87 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 217 TYR 0.020 0.002 TYR A 262 PHE 0.016 0.002 PHE A 328 TRP 0.008 0.001 TRP A 355 HIS 0.009 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (10393) covalent geometry : angle 0.73799 / 0.36 (14100) hydrogen bonds : bond 0.05213 / 3.38 ( 443) hydrogen bonds : angle 4.92969 / 3.44 ( 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 126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7581 (mtm110) REVERT: A 236 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 264 GLN cc_start: 0.7879 (mt0) cc_final: 0.7062 (pt0) REVERT: A 746 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.7881 (tmt) REVERT: A 819 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7965 (mm) REVERT: A 1035 MET cc_start: 0.8395 (ptm) cc_final: 0.8054 (ptm) REVERT: A 1065 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8125 (pp) REVERT: C 227 GLU cc_start: 0.8797 (tp30) cc_final: 0.8328 (tp30) REVERT: C 230 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7250 (mtm-85) outliers start: 32 outliers final: 15 residues processed: 110 average time/residue: 0.5133 time to fit residues: 61.5508 Evaluate side-chains 110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 35 ARG 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 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 1065 LEU 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: 6.9990 chunk 45 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 906 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099560 restraints weight = 14947.909| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.35 r_work: 0.3171 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1828 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= 0.118 Angle : 0.581 8.063 14100 Z= 0.287 Chirality : 0.052 0.442 1541 Planarity : 0.003 0.032 1709 Dihedral : 11.069 139.921 1567 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.56 % Allowed : 14.69 % Favored : 82.75 % 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: -1.08 (0.25), residues: 1150 helix: 0.51 (0.24), residues: 527 sheet: -2.22 (0.39), residues: 149 loop : -1.54 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 217 TYR 0.017 0.001 TYR A 262 PHE 0.010 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/Z covalent geometry : bond 0.00260 / 0.12 (10393) covalent geometry : angle 0.58097 / 0.29 (14100) hydrogen bonds : bond 0.04171 / 2.75 ( 443) hydrogen bonds : angle 4.42464 / 3.08 ( 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 141 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.9243 (p) cc_final: 0.9010 (m) REVERT: A 35 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7633 (mtt90) REVERT: A 264 GLN cc_start: 0.7818 (mt0) cc_final: 0.7036 (pt0) REVERT: A 746 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.7863 (tmt) REVERT: A 819 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7919 (mm) REVERT: A 941 GLN cc_start: 0.8387 (mp10) cc_final: 0.8075 (mp10) REVERT: A 1035 MET cc_start: 0.8286 (ptm) cc_final: 0.7897 (ptm) REVERT: A 1065 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7968 (pp) REVERT: C 202 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7967 (tppp) REVERT: C 227 GLU cc_start: 0.8813 (tp30) cc_final: 0.8413 (tp30) REVERT: C 230 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7339 (mtm-85) outliers start: 27 outliers final: 9 residues processed: 126 average time/residue: 0.4834 time to fit residues: 66.5626 Evaluate side-chains 109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 67 HIS 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 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 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: 4.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3605 r_free = 0.3605 target = 0.122334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094553 restraints weight = 15004.201| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.31 r_work: 0.3093 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10393 Z= 0.249 Angle : 0.686 9.247 14100 Z= 0.339 Chirality : 0.061 0.559 1541 Planarity : 0.004 0.044 1709 Dihedral : 11.050 141.433 1567 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.03 % Allowed : 15.36 % Favored : 81.61 % 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: -0.98 (0.25), residues: 1150 helix: 0.57 (0.24), residues: 522 sheet: -2.24 (0.39), residues: 147 loop : -1.42 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 867 TYR 0.022 0.002 TYR A 262 PHE 0.014 0.001 PHE A 702 TRP 0.008 0.001 TRP A 355 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (10393) covalent geometry : angle 0.68596 / 0.34 (14100) hydrogen bonds : bond 0.04766 / 3.09 ( 443) hydrogen bonds : angle 4.64495 / 3.23 ( 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 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7339 (mtm110) REVERT: A 264 GLN cc_start: 0.7899 (mt0) cc_final: 0.7083 (pt0) REVERT: A 746 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.7881 (tmt) REVERT: A 819 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7911 (mm) REVERT: A 858 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: A 941 GLN cc_start: 0.8373 (mp10) cc_final: 0.8051 (mp10) REVERT: A 1065 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8113 (pp) REVERT: C 227 GLU cc_start: 0.8951 (tp30) cc_final: 0.8623 (tp30) REVERT: C 230 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7317 (mtm-85) outliers start: 32 outliers final: 16 residues processed: 112 average time/residue: 0.4605 time to fit residues: 56.4892 Evaluate side-chains 115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 35 ARG 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 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 746 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100747 restraints weight = 14935.114| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.35 r_work: 0.3188 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10393 Z= 0.110 Angle : 0.566 8.586 14100 Z= 0.279 Chirality : 0.050 0.401 1541 Planarity : 0.003 0.036 1709 Dihedral : 10.902 139.079 1567 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.27 % Allowed : 16.87 % Favored : 80.85 % 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: -0.53 (0.25), residues: 1150 helix: 0.97 (0.24), residues: 521 sheet: -2.05 (0.40), residues: 149 loop : -1.19 (0.28), residues: 480 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 0.008 0.001 PHE A1127 TRP 0.008 0.001 TRP A1193 HIS 0.003 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10393) covalent geometry : angle 0.56628 / 0.28 (14100) hydrogen bonds : bond 0.03991 / 2.63 ( 443) hydrogen bonds : angle 4.25515 / 2.96 ( 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 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.9256 (p) cc_final: 0.8986 (m) REVERT: A 35 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7482 (mtm110) REVERT: A 227 PHE cc_start: 0.7460 (t80) cc_final: 0.7211 (t80) REVERT: A 264 GLN cc_start: 0.7820 (mt0) cc_final: 0.7075 (pt0) REVERT: A 746 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.7844 (tmt) REVERT: A 819 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7909 (mm) REVERT: A 858 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: A 941 GLN cc_start: 0.8408 (mp10) cc_final: 0.8089 (mp10) REVERT: A 949 MET cc_start: 0.8636 (mtp) cc_final: 0.8389 (mtp) REVERT: A 986 MET cc_start: 0.8283 (mtm) cc_final: 0.7918 (mtm) REVERT: A 1035 MET cc_start: 0.8186 (ptm) cc_final: 0.7890 (ptm) REVERT: A 1065 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7959 (pp) REVERT: C 202 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7963 (tppp) REVERT: C 227 GLU cc_start: 0.8975 (tp30) cc_final: 0.8574 (tp30) REVERT: C 230 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7340 (mtm-85) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.4660 time to fit residues: 62.3490 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 476 GLU Chi-restraints excluded: chain A residue 491 VAL 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 857 ASN 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 1065 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=2.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094239 restraints weight = 15020.593| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.34 r_work: 0.3090 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10393 Z= 0.268 Angle : 0.700 9.871 14100 Z= 0.345 Chirality : 0.062 0.603 1541 Planarity : 0.004 0.035 1709 Dihedral : 11.016 141.231 1567 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.46 % Allowed : 17.91 % 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: -0.64 (0.25), residues: 1150 helix: 0.81 (0.24), residues: 516 sheet: -2.12 (0.39), residues: 147 loop : -1.15 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 222 TYR 0.016 0.002 TYR A 794 PHE 0.015 0.002 PHE A 724 TRP 0.009 0.001 TRP A 999 HIS 0.008 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (10393) covalent geometry : angle 0.69973 / 0.35 (14100) hydrogen bonds : bond 0.04738 / 3.05 ( 443) hydrogen bonds : angle 4.59504 / 3.19 ( 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 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7395 (mtm110) REVERT: A 264 GLN cc_start: 0.7897 (mt0) cc_final: 0.7094 (pt0) REVERT: A 746 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.7857 (tmt) REVERT: A 819 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7915 (mm) REVERT: A 941 GLN cc_start: 0.8383 (mp10) cc_final: 0.8067 (mp10) REVERT: A 1065 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8140 (pp) REVERT: C 227 GLU cc_start: 0.9021 (tp30) cc_final: 0.8702 (tp30) REVERT: C 230 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7347 (mtm-85) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.4740 time to fit residues: 57.5927 Evaluate side-chains 111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 236 VAL 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 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 163 GLN 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: 5.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3661 r_free = 0.3661 target = 0.126728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099292 restraints weight = 14821.865| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.30 r_work: 0.3170 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10393 Z= 0.126 Angle : 0.587 9.653 14100 Z= 0.289 Chirality : 0.052 0.407 1541 Planarity : 0.003 0.039 1709 Dihedral : 10.953 139.620 1567 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.99 % Allowed : 18.67 % Favored : 79.34 % 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: -0.34 (0.26), residues: 1150 helix: 1.10 (0.24), residues: 515 sheet: -2.00 (0.40), residues: 149 loop : -1.02 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 222 TYR 0.009 0.001 TYR A 700 PHE 0.010 0.001 PHE A 227 TRP 0.007 0.001 TRP A1193 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10393) covalent geometry : angle 0.58702 / 0.29 (14100) hydrogen bonds : bond 0.04028 / 2.63 ( 443) hydrogen bonds : angle 4.30152 / 2.98 ( 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 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 SER cc_start: 0.9285 (p) cc_final: 0.9018 (m) REVERT: A 35 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7458 (mtm110) REVERT: A 236 VAL cc_start: 0.8217 (t) cc_final: 0.7937 (p) REVERT: A 264 GLN cc_start: 0.7873 (mt0) cc_final: 0.7096 (pt0) REVERT: A 746 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.7867 (tmt) REVERT: A 819 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 858 GLU cc_start: 0.8937 (pt0) cc_final: 0.8344 (mt-10) REVERT: A 941 GLN cc_start: 0.8347 (mp10) cc_final: 0.8048 (mp10) REVERT: A 949 MET cc_start: 0.8634 (mtp) cc_final: 0.8393 (mtp) REVERT: A 1035 MET cc_start: 0.8260 (ptm) cc_final: 0.7984 (ptm) REVERT: A 1065 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7989 (pp) REVERT: C 202 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7955 (tppp) REVERT: C 227 GLU cc_start: 0.9003 (tp30) cc_final: 0.8776 (tp30) REVERT: C 230 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7374 (mtm-85) outliers start: 21 outliers final: 9 residues processed: 109 average time/residue: 0.5007 time to fit residues: 59.8356 Evaluate side-chains 107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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 C residue 202 LYS 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: 6.9990 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3600 r_free = 0.3600 target = 0.121915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094004 restraints weight = 15001.440| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.33 r_work: 0.3086 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10393 Z= 0.270 Angle : 0.709 9.619 14100 Z= 0.350 Chirality : 0.062 0.602 1541 Planarity : 0.004 0.037 1709 Dihedral : 11.108 141.157 1567 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.90 % Allowed : 19.24 % Favored : 78.86 % 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: -0.64 (0.25), residues: 1150 helix: 0.81 (0.24), residues: 522 sheet: -2.12 (0.39), residues: 147 loop : -1.17 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 217 TYR 0.029 0.002 TYR A 262 PHE 0.015 0.002 PHE A 724 TRP 0.010 0.001 TRP A 999 HIS 0.007 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.27 (10393) covalent geometry : angle 0.70905 / 0.35 (14100) hydrogen bonds : bond 0.04705 / 3.02 ( 443) hydrogen bonds : angle 4.58071 / 3.18 ( 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 117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7450 (mtm110) REVERT: A 264 GLN cc_start: 0.7881 (mt0) cc_final: 0.7185 (pt0) REVERT: A 746 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.7866 (tmt) REVERT: A 819 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 858 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: A 941 GLN cc_start: 0.8372 (mp10) cc_final: 0.8054 (mp10) REVERT: A 1035 MET cc_start: 0.8364 (ptm) cc_final: 0.8094 (ptm) REVERT: A 1065 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 1073 ARG cc_start: 0.8250 (ptm160) cc_final: 0.7569 (ptt90) REVERT: C 227 GLU cc_start: 0.9099 (tp30) cc_final: 0.8885 (tp30) REVERT: C 230 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7368 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.5168 time to fit residues: 59.4018 Evaluate side-chains 108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 236 VAL 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 746 MET 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 1065 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3647 r_free = 0.3647 target = 0.125530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097924 restraints weight = 14720.288| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.31 r_work: 0.3150 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10393 Z= 0.151 Angle : 0.618 10.423 14100 Z= 0.306 Chirality : 0.054 0.424 1541 Planarity : 0.003 0.049 1709 Dihedral : 11.041 139.992 1567 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.52 % Allowed : 19.53 % 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: -0.41 (0.26), residues: 1150 helix: 1.03 (0.24), residues: 521 sheet: -1.99 (0.40), residues: 149 loop : -1.08 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 217 TYR 0.011 0.001 TYR A 262 PHE 0.012 0.001 PHE A 227 TRP 0.011 0.001 TRP A 999 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10393) covalent geometry : angle 0.61793 / 0.31 (14100) hydrogen bonds : bond 0.04118 / 2.67 ( 443) hydrogen bonds : angle 4.34358 / 3.01 ( 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 114 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 12 SER cc_start: 0.9312 (p) cc_final: 0.9043 (m) REVERT: A 35 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7406 (mtm110) REVERT: A 64 ASP cc_start: 0.8157 (t0) cc_final: 0.7115 (m-30) REVERT: A 227 PHE cc_start: 0.7407 (t80) cc_final: 0.7011 (t80) REVERT: A 264 GLN cc_start: 0.7860 (mt0) cc_final: 0.7202 (pt0) REVERT: A 391 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: A 746 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.7944 (tmt) REVERT: A 819 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7875 (mm) REVERT: A 858 GLU cc_start: 0.8959 (pt0) cc_final: 0.8344 (mt-10) REVERT: A 941 GLN cc_start: 0.8363 (mp10) cc_final: 0.8058 (mp10) REVERT: A 949 MET cc_start: 0.8643 (mtp) cc_final: 0.8403 (mtp) REVERT: A 1035 MET cc_start: 0.8316 (ptm) cc_final: 0.8018 (ptm) REVERT: A 1065 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8172 (pp) REVERT: C 202 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7940 (tppp) REVERT: C 217 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7117 (mtp180) REVERT: C 227 GLU cc_start: 0.9104 (tp30) cc_final: 0.8901 (tp30) REVERT: C 230 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7436 (mtm-85) outliers start: 16 outliers final: 9 residues processed: 106 average time/residue: 0.4901 time to fit residues: 57.1194 Evaluate side-chains 112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 391 LYS 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 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 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 22 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098146 restraints weight = 14905.170| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.33 r_work: 0.3147 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10393 Z= 0.154 Angle : 0.610 10.254 14100 Z= 0.303 Chirality : 0.054 0.414 1541 Planarity : 0.003 0.035 1709 Dihedral : 10.988 140.672 1567 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.09 % Allowed : 19.43 % Favored : 78.48 % 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: -0.24 (0.26), residues: 1150 helix: 1.17 (0.24), residues: 515 sheet: -1.92 (0.40), residues: 149 loop : -0.95 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 217 TYR 0.020 0.001 TYR A 262 PHE 0.012 0.001 PHE A 702 TRP 0.010 0.001 TRP A 999 HIS 0.004 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10393) covalent geometry : angle 0.61028 / 0.30 (14100) hydrogen bonds : bond 0.04043 / 2.61 ( 443) hydrogen bonds : angle 4.31588 / 2.99 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.70 seconds wall clock time: 61 minutes 36.03 seconds (3696.03 seconds total)