Starting phenix.real_space_refine on Tue Mar 3 16:14:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3f_13179/03_2026/7p3f_13179_neut.cif" } resolution = 3.31 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= -0.002 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 124 5.49 5 S 32 5.16 5 C 3858 2.51 5 N 1280 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 6878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1145 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1028 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "R" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {' ZN': 1, 'ATP': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24 SG CYS A 3 103.479 45.542 34.915 1.00 72.57 S ATOM 48 SG CYS A 6 106.815 43.750 34.928 1.00 73.80 S ATOM 254 SG CYS A 31 106.328 46.744 32.620 1.00 72.42 S ATOM 275 SG CYS A 34 104.522 43.517 31.897 1.00 75.24 S ATOM 2314 SG CYS B 3 38.685 14.665 40.459 1.00 71.45 S ATOM 2338 SG CYS B 6 40.204 11.612 38.607 1.00 68.82 S ATOM 2544 SG CYS B 31 36.880 12.614 37.317 1.00 74.44 S ATOM 2565 SG CYS B 34 37.290 11.235 41.007 1.00 77.60 S Restraints were copied for chains: C, D Time building chain proxies: 1.70, per 1000 atoms: 0.25 Number of scatterers: 6878 At special positions: 0 Unit cell: (129.31, 90.45, 75.71, 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) Zn 4 29.99 S 32 16.00 P 124 15.00 O 1580 8.00 N 1280 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 44 " distance=0.00 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 71 " distance=0.00 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: 0.60 Conformation dependent library (CDL) restraints added in 113.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 6 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 3 " pdb="ZN ZN A 203 " - pdb=" SG CYS A 31 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 6 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 3 " pdb="ZN ZN B 203 " - pdb=" SG CYS B 31 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 6 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 3 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 34 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 6 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 34 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 3 " Number of angles added : 24 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 51.0% alpha, 16.7% beta 41 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.666A pdb=" N VAL A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.720A pdb=" N THR A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 removed outlier: 3.605A pdb=" N GLY A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.289A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.936A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.727A pdb=" N PHE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.666A pdb=" N VAL C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 removed outlier: 3.720A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.605A pdb=" N GLY C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Proline residue: C 112 - end of helix removed outlier: 4.289A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.936A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.727A pdb=" N PHE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.699A pdb=" N VAL B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 96 removed outlier: 3.917A pdb=" N THR B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.756A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.737A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.052A pdb=" N VAL B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.602A pdb=" N GLU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.700A pdb=" N VAL D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 96 removed outlier: 3.917A pdb=" N THR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.756A pdb=" N GLY D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix removed outlier: 3.737A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.052A pdb=" N VAL D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 147 removed outlier: 3.601A pdb=" N GLU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 20 removed outlier: 5.258A pdb=" N VAL A 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN A 30 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 24 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 41 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 43 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 43 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 41 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG D 26 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER D 16 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG D 28 " --> pdb=" O VAL D 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.172A pdb=" N MET A 47 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 20 removed outlier: 5.257A pdb=" N VAL C 13 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN C 30 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 24 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 41 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 43 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 43 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 41 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG B 26 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER B 16 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG B 28 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.172A pdb=" N MET C 47 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 57 214 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 954 1.31 - 1.44: 2264 1.44 - 1.56: 3706 1.56 - 1.69: 238 1.69 - 1.81: 40 Bond restraints: 7202 Sorted by residual: bond pdb=" CA SER A 133 " pdb=" CB SER A 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.44e+01 bond pdb=" CA SER C 133 " pdb=" CB SER C 133 " ideal model delta sigma weight residual 1.532 1.455 0.077 1.56e-02 4.11e+03 2.42e+01 bond pdb=" CA ALA A 140 " pdb=" CB ALA A 140 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.03e+01 bond pdb=" CA ALA C 140 " pdb=" CB ALA C 140 " ideal model delta sigma weight residual 1.528 1.459 0.070 1.56e-02 4.11e+03 2.00e+01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.235 1.185 0.050 1.15e-02 7.56e+03 1.87e+01 ... (remaining 7197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 9087 2.06 - 4.12: 971 4.12 - 6.19: 129 6.19 - 8.25: 33 8.25 - 10.31: 6 Bond angle restraints: 10226 Sorted by residual: angle pdb=" PB ATP B 201 " pdb=" O3B ATP B 201 " pdb=" PG ATP B 201 " ideal model delta sigma weight residual 139.87 131.73 8.14 1.00e+00 1.00e+00 6.62e+01 angle pdb=" PB ATP D 201 " pdb=" O3B ATP D 201 " pdb=" PG ATP D 201 " ideal model delta sigma weight residual 139.87 131.75 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" PB DTP B 202 " pdb=" O3B DTP B 202 " pdb=" PG DTP B 202 " ideal model delta sigma weight residual 139.87 131.80 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" PB DTP D 202 " pdb=" O3B DTP D 202 " pdb=" PG DTP D 202 " ideal model delta sigma weight residual 139.87 131.82 8.05 1.00e+00 1.00e+00 6.49e+01 angle pdb=" PB DTP C 202 " pdb=" O3B DTP C 202 " pdb=" PG DTP C 202 " ideal model delta sigma weight residual 139.87 132.55 7.32 1.00e+00 1.00e+00 5.36e+01 ... (remaining 10221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 3414 28.18 - 56.36: 691 56.36 - 84.53: 114 84.53 - 112.71: 5 112.71 - 140.89: 2 Dihedral angle restraints: 4226 sinusoidal: 2522 harmonic: 1704 Sorted by residual: dihedral pdb=" C GLU D 42 " pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta harmonic sigma weight residual -122.60 -112.04 -10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C GLU B 42 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" CB GLU B 42 " ideal model delta harmonic sigma weight residual -122.60 -112.09 -10.51 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" C THR C 19 " pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta harmonic sigma weight residual -122.00 -132.37 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 846 0.074 - 0.147: 229 0.147 - 0.220: 62 0.220 - 0.293: 15 0.293 - 0.367: 4 Chirality restraints: 1156 Sorted by residual: chirality pdb=" CA THR C 19 " pdb=" N THR C 19 " pdb=" C THR C 19 " pdb=" CB THR C 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA THR A 19 " pdb=" N THR A 19 " pdb=" C THR A 19 " pdb=" CB THR A 19 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1153 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP D 201 " -0.096 2.00e-02 2.50e+03 4.13e-02 4.69e+01 pdb=" C2 ATP D 201 " 0.014 2.00e-02 2.50e+03 pdb=" C4 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" C5 ATP D 201 " 0.024 2.00e-02 2.50e+03 pdb=" C6 ATP D 201 " -0.005 2.00e-02 2.50e+03 pdb=" C8 ATP D 201 " 0.029 2.00e-02 2.50e+03 pdb=" N1 ATP D 201 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ATP D 201 " 0.030 2.00e-02 2.50e+03 pdb=" N6 ATP D 201 " -0.070 2.00e-02 2.50e+03 pdb=" N7 ATP D 201 " 0.031 2.00e-02 2.50e+03 pdb=" N9 ATP D 201 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP B 201 " 0.096 2.00e-02 2.50e+03 4.12e-02 4.66e+01 pdb=" C2 ATP B 201 " -0.014 2.00e-02 2.50e+03 pdb=" C4 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" C5 ATP B 201 " -0.024 2.00e-02 2.50e+03 pdb=" C6 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" C8 ATP B 201 " -0.029 2.00e-02 2.50e+03 pdb=" N1 ATP B 201 " 0.005 2.00e-02 2.50e+03 pdb=" N3 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N6 ATP B 201 " 0.069 2.00e-02 2.50e+03 pdb=" N7 ATP B 201 " -0.030 2.00e-02 2.50e+03 pdb=" N9 ATP B 201 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 21 " -0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C ASP D 21 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP D 21 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY D 22 " -0.028 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1219 2.77 - 3.31: 5907 3.31 - 3.84: 12082 3.84 - 4.37: 15240 4.37 - 4.90: 22227 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" OD2 ASP A 104 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C 101 " pdb=" OD2 ASP C 104 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG B 68 " pdb=" OE2 GLU B 78 " model vdw 2.286 3.120 nonbonded pdb=" NH1 ARG D 68 " pdb=" OE2 GLU D 78 " model vdw 2.286 3.120 nonbonded pdb=" O ALA B 70 " pdb=" NH1 ARG B 123 " model vdw 2.420 3.120 ... (remaining 56670 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.010 0.195 7218 Z= 0.629 Angle : 1.335 13.022 10252 Z= 0.926 Chirality : 0.077 0.367 1156 Planarity : 0.008 0.049 940 Dihedral : 25.952 140.891 3110 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.59 % Allowed : 5.95 % Favored : 92.46 % Cbeta Deviations : 1.08 % 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: -1.22 (0.35), residues: 580 helix: -0.04 (0.31), residues: 270 sheet: -1.47 (0.55), residues: 96 loop : -1.31 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 36 TYR 0.011 0.002 TYR B 121 PHE 0.043 0.004 PHE B 38 HIS 0.013 0.003 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 7202) covalent geometry : angle 1.31782 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.16887 ( 317) hydrogen bonds : angle 9.31485 ( 832) metal coordination : bond 0.09406 ( 16) metal coordination : angle 4.65050 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.222 Fit side-chains REVERT: A 17 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7557 (ttp-110) REVERT: A 25 ILE cc_start: 0.8908 (tt) cc_final: 0.8585 (tt) REVERT: A 134 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (pt) REVERT: C 17 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7490 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 0.1172 time to fit residues: 19.1098 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132963 restraints weight = 8326.314| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.80 r_work: 0.3365 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7218 Z= 0.173 Angle : 0.611 6.040 10252 Z= 0.352 Chirality : 0.038 0.175 1156 Planarity : 0.005 0.046 940 Dihedral : 28.448 138.289 2012 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.99 % Allowed : 12.50 % Favored : 86.51 % 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: -0.87 (0.35), residues: 580 helix: 0.26 (0.31), residues: 276 sheet: -1.37 (0.47), residues: 114 loop : -1.09 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 123 TYR 0.015 0.002 TYR B 121 PHE 0.011 0.001 PHE A 124 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7202) covalent geometry : angle 0.59230 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.06325 ( 317) hydrogen bonds : angle 3.82815 ( 832) metal coordination : bond 0.00393 ( 16) metal coordination : angle 3.17152 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.199 Fit side-chains REVERT: A 26 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7499 (ttp80) REVERT: A 28 ARG cc_start: 0.9072 (tpt90) cc_final: 0.8791 (tpt90) REVERT: A 42 GLU cc_start: 0.7778 (pt0) cc_final: 0.7336 (pt0) REVERT: C 28 ARG cc_start: 0.9065 (tpt90) cc_final: 0.8766 (tpt90) REVERT: C 42 GLU cc_start: 0.7787 (pt0) cc_final: 0.7519 (pt0) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.1210 time to fit residues: 15.7052 Evaluate side-chains 97 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.191792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125420 restraints weight = 8142.696| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.91 r_work: 0.3157 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7218 Z= 0.278 Angle : 0.668 7.746 10252 Z= 0.370 Chirality : 0.040 0.166 1156 Planarity : 0.006 0.048 940 Dihedral : 28.441 143.588 2010 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.77 % Allowed : 16.67 % Favored : 79.56 % 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: -1.03 (0.35), residues: 580 helix: -0.04 (0.30), residues: 272 sheet: -1.11 (0.49), residues: 104 loop : -1.12 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 123 TYR 0.011 0.003 TYR C 121 PHE 0.019 0.002 PHE A 124 HIS 0.005 0.002 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 7202) covalent geometry : angle 0.64419 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.06258 ( 317) hydrogen bonds : angle 4.03913 ( 832) metal coordination : bond 0.00514 ( 16) metal coordination : angle 3.68399 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8144 (mmt180) cc_final: 0.6878 (ttp-110) REVERT: A 28 ARG cc_start: 0.8977 (tpt90) cc_final: 0.8463 (tpt90) REVERT: A 42 GLU cc_start: 0.7881 (pt0) cc_final: 0.7590 (pt0) REVERT: C 17 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7002 (ttp-110) REVERT: C 28 ARG cc_start: 0.9027 (tpt90) cc_final: 0.8454 (tpt90) REVERT: C 42 GLU cc_start: 0.7959 (pt0) cc_final: 0.7716 (pt0) REVERT: B 26 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7414 (ttp-170) REVERT: B 30 GLN cc_start: 0.7966 (tt0) cc_final: 0.7145 (tt0) REVERT: D 30 GLN cc_start: 0.7978 (tt0) cc_final: 0.7337 (tt0) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.1259 time to fit residues: 18.0724 Evaluate side-chains 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130358 restraints weight = 8235.106| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.73 r_work: 0.3247 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7218 Z= 0.168 Angle : 0.570 6.327 10252 Z= 0.321 Chirality : 0.035 0.141 1156 Planarity : 0.004 0.043 940 Dihedral : 27.912 142.220 2010 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 18.06 % Favored : 79.56 % 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: -0.65 (0.35), residues: 580 helix: 0.30 (0.31), residues: 274 sheet: -0.91 (0.50), residues: 104 loop : -0.98 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.009 0.002 TYR D 121 PHE 0.011 0.002 PHE A 124 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7202) covalent geometry : angle 0.55242 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05312 ( 317) hydrogen bonds : angle 3.65487 ( 832) metal coordination : bond 0.00261 ( 16) metal coordination : angle 2.98275 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8946 (tpt90) cc_final: 0.8575 (tpt90) REVERT: A 42 GLU cc_start: 0.7776 (pt0) cc_final: 0.7259 (pt0) REVERT: C 17 ARG cc_start: 0.8092 (mmt180) cc_final: 0.6809 (ttp-110) REVERT: C 42 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: B 26 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7317 (ttp-170) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.1198 time to fit residues: 17.2203 Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN D 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.196488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131282 restraints weight = 8233.126| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.05 r_work: 0.3304 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7218 Z= 0.162 Angle : 0.563 6.262 10252 Z= 0.315 Chirality : 0.035 0.155 1156 Planarity : 0.004 0.042 940 Dihedral : 27.737 145.008 2010 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 18.45 % Favored : 78.77 % 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: -0.39 (0.36), residues: 580 helix: 0.46 (0.32), residues: 274 sheet: -0.78 (0.51), residues: 104 loop : -0.79 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.009 0.001 TYR D 121 PHE 0.011 0.001 PHE A 124 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7202) covalent geometry : angle 0.54484 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05133 ( 317) hydrogen bonds : angle 3.55426 ( 832) metal coordination : bond 0.00244 ( 16) metal coordination : angle 2.98401 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.150 Fit side-chains REVERT: A 28 ARG cc_start: 0.8916 (tpt90) cc_final: 0.8422 (tpt-90) REVERT: A 42 GLU cc_start: 0.7759 (pt0) cc_final: 0.7313 (pt0) REVERT: C 17 ARG cc_start: 0.8134 (mmt180) cc_final: 0.6839 (ttp-110) REVERT: C 28 ARG cc_start: 0.8952 (tpt90) cc_final: 0.8322 (tpt90) REVERT: C 42 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: B 26 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7169 (ttp-170) REVERT: B 30 GLN cc_start: 0.7787 (tt0) cc_final: 0.7304 (tt0) REVERT: D 8 HIS cc_start: 0.7725 (t70) cc_final: 0.7462 (t70) REVERT: D 30 GLN cc_start: 0.7733 (tt0) cc_final: 0.7377 (mt0) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 0.1216 time to fit residues: 16.8182 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.193805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127402 restraints weight = 8242.232| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.85 r_work: 0.3189 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7218 Z= 0.233 Angle : 0.617 6.999 10252 Z= 0.340 Chirality : 0.037 0.161 1156 Planarity : 0.005 0.043 940 Dihedral : 27.908 144.449 2010 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.97 % Allowed : 18.45 % Favored : 77.58 % 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: -0.69 (0.35), residues: 580 helix: 0.15 (0.32), residues: 274 sheet: -0.89 (0.50), residues: 104 loop : -0.83 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.008 0.002 TYR B 121 PHE 0.015 0.002 PHE A 124 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 7202) covalent geometry : angle 0.59654 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05446 ( 317) hydrogen bonds : angle 3.81688 ( 832) metal coordination : bond 0.00445 ( 16) metal coordination : angle 3.27891 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.203 Fit side-chains REVERT: A 42 GLU cc_start: 0.7875 (pt0) cc_final: 0.7548 (pt0) REVERT: C 17 ARG cc_start: 0.8226 (mmt180) cc_final: 0.6945 (ttp-110) REVERT: C 28 ARG cc_start: 0.8985 (tpt90) cc_final: 0.8775 (tpt90) REVERT: B 30 GLN cc_start: 0.7858 (tt0) cc_final: 0.7373 (tt0) REVERT: D 30 GLN cc_start: 0.7813 (tt0) cc_final: 0.7429 (tt0) outliers start: 20 outliers final: 17 residues processed: 111 average time/residue: 0.1127 time to fit residues: 15.4684 Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.196943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130980 restraints weight = 8239.473| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.71 r_work: 0.3254 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7218 Z= 0.149 Angle : 0.564 7.734 10252 Z= 0.315 Chirality : 0.034 0.153 1156 Planarity : 0.004 0.040 940 Dihedral : 27.490 143.774 2010 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.17 % Allowed : 19.05 % Favored : 77.78 % 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: -0.32 (0.36), residues: 580 helix: 0.52 (0.32), residues: 272 sheet: -0.78 (0.50), residues: 104 loop : -0.71 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 12 TYR 0.009 0.001 TYR B 121 PHE 0.009 0.001 PHE C 124 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7202) covalent geometry : angle 0.54870 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04826 ( 317) hydrogen bonds : angle 3.66244 ( 832) metal coordination : bond 0.00212 ( 16) metal coordination : angle 2.78737 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.293 Fit side-chains REVERT: A 28 ARG cc_start: 0.8970 (tpt90) cc_final: 0.8472 (tpt90) REVERT: A 42 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: A 86 GLN cc_start: 0.8360 (mm110) cc_final: 0.7994 (mm110) REVERT: B 26 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7293 (ttp-170) REVERT: B 30 GLN cc_start: 0.7811 (tt0) cc_final: 0.7374 (tt0) REVERT: D 8 HIS cc_start: 0.7752 (t70) cc_final: 0.7517 (t70) REVERT: D 30 GLN cc_start: 0.7764 (tt0) cc_final: 0.7447 (mt0) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.1054 time to fit residues: 15.3834 Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.194284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127784 restraints weight = 8255.349| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.83 r_work: 0.3195 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7218 Z= 0.212 Angle : 0.607 6.967 10252 Z= 0.335 Chirality : 0.036 0.146 1156 Planarity : 0.005 0.042 940 Dihedral : 27.587 143.526 2010 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.37 % Allowed : 17.86 % Favored : 78.77 % 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: -0.39 (0.35), residues: 580 helix: 0.41 (0.32), residues: 272 sheet: -0.89 (0.49), residues: 104 loop : -0.62 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 123 TYR 0.007 0.002 TYR B 121 PHE 0.014 0.002 PHE A 124 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7202) covalent geometry : angle 0.58758 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.05125 ( 317) hydrogen bonds : angle 3.79403 ( 832) metal coordination : bond 0.00371 ( 16) metal coordination : angle 3.16656 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.195 Fit side-chains REVERT: A 28 ARG cc_start: 0.8969 (tpt90) cc_final: 0.8702 (tpt90) REVERT: A 42 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: C 17 ARG cc_start: 0.8209 (mmt180) cc_final: 0.6947 (ttp-110) REVERT: C 28 ARG cc_start: 0.8953 (tpt90) cc_final: 0.8751 (tpt90) REVERT: B 30 GLN cc_start: 0.7834 (tt0) cc_final: 0.7388 (tt0) REVERT: D 30 GLN cc_start: 0.7801 (tt0) cc_final: 0.7457 (tt0) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.1077 time to fit residues: 14.6170 Evaluate side-chains 110 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.198010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131949 restraints weight = 8280.915| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.81 r_work: 0.3259 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7218 Z= 0.142 Angle : 0.564 8.251 10252 Z= 0.315 Chirality : 0.034 0.144 1156 Planarity : 0.004 0.040 940 Dihedral : 27.180 143.096 2010 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.78 % Allowed : 19.05 % Favored : 78.17 % 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: -0.06 (0.35), residues: 580 helix: 0.73 (0.32), residues: 272 sheet: -0.22 (0.51), residues: 94 loop : -0.83 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 12 TYR 0.007 0.001 TYR D 121 PHE 0.008 0.001 PHE A 124 HIS 0.002 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7202) covalent geometry : angle 0.54895 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04570 ( 317) hydrogen bonds : angle 3.63983 ( 832) metal coordination : bond 0.00185 ( 16) metal coordination : angle 2.74069 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.220 Fit side-chains REVERT: A 28 ARG cc_start: 0.8971 (tpt90) cc_final: 0.8732 (tpt90) REVERT: A 42 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: C 17 ARG cc_start: 0.8171 (mmt180) cc_final: 0.6900 (ttp-110) REVERT: B 30 GLN cc_start: 0.7784 (tt0) cc_final: 0.7371 (tt0) REVERT: D 8 HIS cc_start: 0.7666 (t70) cc_final: 0.7432 (t70) REVERT: D 30 GLN cc_start: 0.7734 (tt0) cc_final: 0.7482 (mt0) outliers start: 14 outliers final: 10 residues processed: 107 average time/residue: 0.1005 time to fit residues: 13.6668 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.0470 chunk 25 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 86 GLN B 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.200053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135200 restraints weight = 8178.634| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.78 r_work: 0.3304 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7218 Z= 0.132 Angle : 0.550 8.361 10252 Z= 0.308 Chirality : 0.034 0.132 1156 Planarity : 0.004 0.040 940 Dihedral : 26.916 142.957 2010 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 19.64 % Favored : 78.17 % 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: -0.01 (0.36), residues: 580 helix: 0.72 (0.32), residues: 274 sheet: -0.62 (0.51), residues: 104 loop : -0.49 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 17 TYR 0.007 0.001 TYR B 121 PHE 0.010 0.001 PHE D 137 HIS 0.002 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7202) covalent geometry : angle 0.53551 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04419 ( 317) hydrogen bonds : angle 3.60037 ( 832) metal coordination : bond 0.00171 ( 16) metal coordination : angle 2.62386 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.223 Fit side-chains REVERT: A 28 ARG cc_start: 0.8976 (tpt90) cc_final: 0.8713 (tpt90) REVERT: A 42 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: C 30 GLN cc_start: 0.8238 (tt0) cc_final: 0.7678 (tm-30) REVERT: C 42 GLU cc_start: 0.7147 (pt0) cc_final: 0.6945 (pt0) REVERT: B 30 GLN cc_start: 0.7710 (tt0) cc_final: 0.7310 (tt0) REVERT: D 30 GLN cc_start: 0.7690 (tt0) cc_final: 0.7444 (mt0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.0995 time to fit residues: 13.1508 Evaluate side-chains 105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 8 HIS D 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.199327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134648 restraints weight = 8334.160| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.72 r_work: 0.3296 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7218 Z= 0.136 Angle : 0.540 7.822 10252 Z= 0.302 Chirality : 0.033 0.126 1156 Planarity : 0.004 0.039 940 Dihedral : 26.881 142.903 2010 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.98 % Allowed : 19.84 % Favored : 78.17 % 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: 0.07 (0.36), residues: 580 helix: 0.74 (0.32), residues: 274 sheet: -0.55 (0.49), residues: 106 loop : -0.39 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 60 TYR 0.007 0.001 TYR B 121 PHE 0.008 0.001 PHE A 58 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7202) covalent geometry : angle 0.52795 (10226) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04217 ( 317) hydrogen bonds : angle 3.56295 ( 832) metal coordination : bond 0.00191 ( 16) metal coordination : angle 2.42516 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.04 seconds wall clock time: 31 minutes 12.08 seconds (1872.08 seconds total)