Starting phenix.real_space_refine on Fri Sep 11 02:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3f_13179/09_2026/7p3f_13179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3f_13179/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7p3f_13179/09_2026/7p3f_13179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3f_13179/09_2026/7p3f_13179_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3f_13179/09_2026/7p3f_13179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3f_13179/09_2026/7p3f_13179.map" } 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-2.2.1-6174/lib/python3.11/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: 1.36, per 1000 atoms: 0.20 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: 0.42 Conformation dependent library (CDL) restraints added in 227.8 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: 0.94 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: 1.04 Time building geometry restraints manager: 0.59 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: 9153 2.06 - 4.12: 915 4.12 - 6.19: 118 6.19 - 8.25: 34 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 - 0.073: 850 0.073 - 0.147: 225 0.147 - 0.220: 61 0.220 - 0.293: 16 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.100 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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= 0.652 Angle : 1.299 13.022 10252 Z= 0.935 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/Z covalent geometry : bond 0.00902 / 0.63 ( 7202) covalent geometry : angle 1.28128 / 0.94 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.16887 / 11.74 ( 317) hydrogen bonds : angle 9.31485 / 6.64 ( 832) metal coordination : bond 0.09406 / 6.38 ( 16) metal coordination : angle 4.65050 / 2.89 ( 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 : 0.221 Fit side-chains REVERT: A 17 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7555 (ttp-110) REVERT: A 25 ILE cc_start: 0.8908 (tt) cc_final: 0.8584 (tt) REVERT: A 134 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8140 (pt) REVERT: C 17 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7489 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 132 average time/residue: 0.1054 time to fit residues: 17.4131 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 : 0.166 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 50.0000 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... A 86 GLN C 86 GLN D 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133865 restraints weight = 8199.455| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.74 r_work: 0.3396 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1614 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= 0.177 Angle : 0.711 8.971 10252 Z= 0.404 Chirality : 0.048 0.231 1156 Planarity : 0.005 0.054 940 Dihedral : 28.860 142.561 2012 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.59 % Allowed : 13.49 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.35), residues: 580 helix: 0.25 (0.31), residues: 272 sheet: -1.24 (0.49), residues: 114 loop : -1.20 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 123 TYR 0.019 0.003 TYR D 121 PHE 0.011 0.001 PHE A 124 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 ( 7202) covalent geometry : angle 0.69751 / 0.40 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.08638 / 6.37 ( 317) hydrogen bonds : angle 4.20842 / 2.92 ( 832) metal coordination : bond 0.00609 / 0.42 ( 16) metal coordination : angle 2.94960 / 1.97 ( 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 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.167 Fit side-chains REVERT: D 2 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8412 (m90) outliers start: 8 outliers final: 5 residues processed: 108 average time/residue: 0.0903 time to fit residues: 12.3161 Evaluate side-chains 100 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 2 HIS 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: 3.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN D 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.190752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125317 restraints weight = 8164.928| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.81 r_work: 0.3261 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 7218 Z= 0.320 Angle : 0.770 10.200 10252 Z= 0.423 Chirality : 0.048 0.211 1156 Planarity : 0.007 0.055 940 Dihedral : 28.871 138.448 2012 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.98 % Allowed : 16.47 % Favored : 80.56 % 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: -1.27 (0.34), residues: 580 helix: -0.42 (0.29), residues: 280 sheet: -0.96 (0.50), residues: 104 loop : -1.11 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 123 TYR 0.014 0.004 TYR C 121 PHE 0.022 0.003 PHE A 124 HIS 0.012 0.003 HIS D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.32 ( 7202) covalent geometry : angle 0.74161 / 0.42 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.07415 / 5.40 ( 317) hydrogen bonds : angle 4.25403 / 2.97 ( 832) metal coordination : bond 0.00661 / 0.39 ( 16) metal coordination : angle 4.32080 / 2.65 ( 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 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.207 Fit side-chains REVERT: A 17 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7065 (ttp-110) REVERT: A 132 ASP cc_start: 0.8927 (t0) cc_final: 0.8683 (t0) REVERT: C 132 ASP cc_start: 0.8924 (t0) cc_final: 0.8696 (t0) REVERT: B 30 GLN cc_start: 0.8015 (tt0) cc_final: 0.7314 (tt0) REVERT: D 30 GLN cc_start: 0.8016 (tt0) cc_final: 0.7279 (tt0) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.1053 time to fit residues: 14.3129 Evaluate side-chains 106 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 134 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 52 SER 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 1 MET Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 44 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 40.0000 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN D 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.194829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129839 restraints weight = 8136.851| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.86 r_work: 0.3322 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2377 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= 0.146 Angle : 0.624 8.367 10252 Z= 0.358 Chirality : 0.042 0.226 1156 Planarity : 0.005 0.049 940 Dihedral : 28.428 140.306 2012 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 18.65 % Favored : 79.17 % 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: -0.82 (0.35), residues: 580 helix: 0.25 (0.32), residues: 274 sheet: -1.30 (0.47), residues: 114 loop : -0.98 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.015 0.002 TYR B 121 PHE 0.011 0.002 PHE A 124 HIS 0.005 0.001 HIS D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 7202) covalent geometry : angle 0.60073 / 0.36 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.06454 / 4.89 ( 317) hydrogen bonds : angle 3.84120 / 2.68 ( 832) metal coordination : bond 0.00330 / 0.23 ( 16) metal coordination : angle 3.54403 / 2.23 ( 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 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.144 Fit side-chains REVERT: A 17 ARG cc_start: 0.8149 (mmt180) cc_final: 0.6845 (ttp-110) REVERT: C 17 ARG cc_start: 0.8166 (mmt180) cc_final: 0.6950 (ttp-110) REVERT: C 42 GLU cc_start: 0.7602 (pt0) cc_final: 0.7168 (pt0) REVERT: B 30 GLN cc_start: 0.7961 (tt0) cc_final: 0.7238 (tt0) REVERT: D 8 HIS cc_start: 0.7590 (t70) cc_final: 0.7365 (t70) REVERT: D 30 GLN cc_start: 0.7990 (tt0) cc_final: 0.7386 (tt0) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.1051 time to fit residues: 14.3842 Evaluate side-chains 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain C residue 52 SER 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 D residue 2 HIS Chi-restraints excluded: chain D residue 26 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 HIS ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.193337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127546 restraints weight = 8165.199| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.80 r_work: 0.3300 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7218 Z= 0.188 Angle : 0.622 7.502 10252 Z= 0.355 Chirality : 0.042 0.213 1156 Planarity : 0.005 0.049 940 Dihedral : 28.398 143.126 2010 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.77 % Allowed : 16.47 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.35), residues: 580 helix: 0.29 (0.32), residues: 274 sheet: -0.86 (0.49), residues: 104 loop : -0.95 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 123 TYR 0.009 0.002 TYR D 121 PHE 0.014 0.002 PHE A 124 HIS 0.003 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 7202) covalent geometry : angle 0.60368 / 0.35 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.06325 / 4.74 ( 317) hydrogen bonds : angle 3.82096 / 2.67 ( 832) metal coordination : bond 0.00380 / 0.28 ( 16) metal coordination : angle 3.17370 / 2.13 ( 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 124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.198 Fit side-chains REVERT: A 17 ARG cc_start: 0.8182 (mmt180) cc_final: 0.6897 (ttp-110) REVERT: C 17 ARG cc_start: 0.8161 (mmt180) cc_final: 0.7033 (ttp-110) REVERT: B 30 GLN cc_start: 0.7986 (tt0) cc_final: 0.7273 (tt0) REVERT: D 2 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8075 (m90) REVERT: D 8 HIS cc_start: 0.7767 (t70) cc_final: 0.7525 (t70) outliers start: 19 outliers final: 14 residues processed: 120 average time/residue: 0.0947 time to fit residues: 14.4716 Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 40 THR 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 30 GLN 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 24 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 26 ARG 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: 0.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 40.0000 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.196706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129930 restraints weight = 8164.273| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.89 r_work: 0.3319 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7218 Z= 0.138 Angle : 0.594 6.965 10252 Z= 0.341 Chirality : 0.040 0.213 1156 Planarity : 0.004 0.046 940 Dihedral : 28.047 144.945 2010 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % 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: -0.52 (0.35), residues: 580 helix: 0.58 (0.32), residues: 274 sheet: -1.23 (0.47), residues: 114 loop : -0.92 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.012 0.002 TYR B 121 PHE 0.009 0.001 PHE A 58 HIS 0.009 0.001 HIS D 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 ( 7202) covalent geometry : angle 0.57783 / 0.34 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.06011 / 4.59 ( 317) hydrogen bonds : angle 3.66560 / 2.57 ( 832) metal coordination : bond 0.00290 / 0.22 ( 16) metal coordination : angle 2.94027 / 2.01 ( 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 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.165 Fit side-chains REVERT: A 17 ARG cc_start: 0.8100 (mmt180) cc_final: 0.6789 (ttp-110) REVERT: C 17 ARG cc_start: 0.8118 (mmt180) cc_final: 0.6799 (ttp-110) REVERT: B 30 GLN cc_start: 0.7895 (tt0) cc_final: 0.7178 (tt0) REVERT: D 8 HIS cc_start: 0.7759 (t70) cc_final: 0.7509 (t70) REVERT: D 30 GLN cc_start: 0.7757 (tt0) cc_final: 0.7328 (tt0) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.0997 time to fit residues: 13.4358 Evaluate side-chains 103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 24 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 40.0000 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 50.0000 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.194869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129369 restraints weight = 8131.460| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.92 r_work: 0.3290 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7218 Z= 0.174 Angle : 0.603 7.093 10252 Z= 0.341 Chirality : 0.040 0.199 1156 Planarity : 0.005 0.046 940 Dihedral : 27.999 146.473 2010 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.17 % Allowed : 17.46 % Favored : 79.37 % 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: -0.42 (0.35), residues: 580 helix: 0.49 (0.32), residues: 274 sheet: -0.76 (0.49), residues: 104 loop : -0.90 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 123 TYR 0.005 0.001 TYR D 121 PHE 0.013 0.002 PHE A 124 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 7202) covalent geometry : angle 0.58551 / 0.34 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.06032 / 4.54 ( 317) hydrogen bonds : angle 3.66674 / 2.58 ( 832) metal coordination : bond 0.00320 / 0.23 ( 16) metal coordination : angle 3.05113 / 2.07 ( 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 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8114 (mmt180) cc_final: 0.6808 (ttp-110) REVERT: C 17 ARG cc_start: 0.8083 (mmt180) cc_final: 0.6800 (ttp-110) REVERT: C 42 GLU cc_start: 0.7518 (pt0) cc_final: 0.7008 (pt0) REVERT: B 30 GLN cc_start: 0.7920 (tt0) cc_final: 0.7343 (tt0) REVERT: D 8 HIS cc_start: 0.7731 (t70) cc_final: 0.7243 (t70) REVERT: D 30 GLN cc_start: 0.7783 (tt0) cc_final: 0.7346 (tt0) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.0961 time to fit residues: 13.7320 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 24 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 50.0000 chunk 2 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.195106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132439 restraints weight = 8192.541| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.21 r_work: 0.3266 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7218 Z= 0.152 Angle : 0.592 6.849 10252 Z= 0.337 Chirality : 0.039 0.190 1156 Planarity : 0.004 0.045 940 Dihedral : 27.878 147.199 2010 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.57 % Allowed : 17.46 % Favored : 78.97 % 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: -0.37 (0.35), residues: 580 helix: 0.50 (0.32), residues: 276 sheet: -0.76 (0.49), residues: 104 loop : -0.83 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 145 TYR 0.008 0.001 TYR B 121 PHE 0.010 0.001 PHE A 124 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 7202) covalent geometry : angle 0.57569 / 0.34 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05825 / 4.42 ( 317) hydrogen bonds : angle 3.63612 / 2.56 ( 832) metal coordination : bond 0.00286 / 0.21 ( 16) metal coordination : angle 2.89725 / 1.98 ( 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 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.135 Fit side-chains REVERT: A 17 ARG cc_start: 0.8093 (mmt180) cc_final: 0.6745 (ttp-110) REVERT: C 17 ARG cc_start: 0.8083 (mmt180) cc_final: 0.6731 (ttp-110) REVERT: C 42 GLU cc_start: 0.7529 (pt0) cc_final: 0.6999 (pt0) REVERT: B 30 GLN cc_start: 0.7897 (tt0) cc_final: 0.7323 (tt0) REVERT: D 30 GLN cc_start: 0.7770 (tt0) cc_final: 0.7364 (tt0) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.0999 time to fit residues: 13.9318 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 24 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.7687 > 50:) chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.196370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133862 restraints weight = 8152.407| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.09 r_work: 0.3295 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7218 Z= 0.138 Angle : 0.584 7.344 10252 Z= 0.333 Chirality : 0.039 0.190 1156 Planarity : 0.004 0.044 940 Dihedral : 27.751 147.723 2010 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.37 % Allowed : 18.65 % Favored : 77.98 % 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 (0.35), residues: 580 helix: 0.53 (0.33), residues: 274 sheet: -0.24 (0.52), residues: 94 loop : -1.11 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.008 0.001 TYR D 121 PHE 0.009 0.001 PHE C 58 HIS 0.003 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 ( 7202) covalent geometry : angle 0.56852 / 0.33 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05657 / 4.32 ( 317) hydrogen bonds : angle 3.62064 / 2.56 ( 832) metal coordination : bond 0.00260 / 0.20 ( 16) metal coordination : angle 2.80750 / 1.91 ( 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 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.223 Fit side-chains REVERT: A 17 ARG cc_start: 0.8109 (mmt180) cc_final: 0.6761 (ttp-110) REVERT: C 17 ARG cc_start: 0.8077 (mmt180) cc_final: 0.6782 (ttp-110) REVERT: C 42 GLU cc_start: 0.7407 (pt0) cc_final: 0.6799 (pt0) REVERT: B 30 GLN cc_start: 0.7881 (tt0) cc_final: 0.7330 (tt0) REVERT: D 30 GLN cc_start: 0.7774 (tt0) cc_final: 0.7439 (mt0) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.1013 time to fit residues: 13.6128 Evaluate side-chains 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 24 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 40.0000 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.196460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130300 restraints weight = 8209.432| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.58 r_work: 0.3252 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7218 Z= 0.146 Angle : 0.604 8.121 10252 Z= 0.342 Chirality : 0.039 0.193 1156 Planarity : 0.004 0.044 940 Dihedral : 27.660 148.308 2010 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 20.24 % Favored : 77.18 % 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: -0.26 (0.35), residues: 580 helix: 0.60 (0.32), residues: 272 sheet: -0.27 (0.52), residues: 94 loop : -1.02 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 7 TYR 0.006 0.001 TYR B 121 PHE 0.010 0.001 PHE A 124 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 7202) covalent geometry : angle 0.58849 / 0.34 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05593 / 4.25 ( 317) hydrogen bonds : angle 3.62696 / 2.58 ( 832) metal coordination : bond 0.00267 / 0.19 ( 16) metal coordination : angle 2.86267 / 1.94 ( 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 113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8141 (mmt180) cc_final: 0.6781 (ttp-110) REVERT: C 17 ARG cc_start: 0.8137 (mmt180) cc_final: 0.6858 (ttp-110) REVERT: C 42 GLU cc_start: 0.7385 (pt0) cc_final: 0.6799 (pt0) REVERT: B 30 GLN cc_start: 0.7900 (tt0) cc_final: 0.7366 (tt0) REVERT: D 30 GLN cc_start: 0.7774 (tt0) cc_final: 0.7474 (mt0) outliers start: 13 outliers final: 12 residues processed: 107 average time/residue: 0.0990 time to fit residues: 13.3294 Evaluate side-chains 110 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 24 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 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: 1.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 58 optimal weight: 40.0000 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN C 86 GLN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.195606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132526 restraints weight = 8083.693| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.08 r_work: 0.3277 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7218 Z= 0.151 Angle : 0.588 7.541 10252 Z= 0.332 Chirality : 0.039 0.194 1156 Planarity : 0.004 0.045 940 Dihedral : 27.632 148.693 2010 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.58 % Allowed : 20.04 % Favored : 77.38 % 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: -0.35 (0.35), residues: 580 helix: 0.53 (0.32), residues: 272 sheet: -0.83 (0.49), residues: 104 loop : -0.75 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 36 TYR 0.006 0.001 TYR B 121 PHE 0.011 0.001 PHE A 124 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 7202) covalent geometry : angle 0.57253 / 0.33 (10226) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.05485 / 4.16 ( 317) hydrogen bonds : angle 3.62334 / 2.56 ( 832) metal coordination : bond 0.00290 / 0.20 ( 16) metal coordination : angle 2.85747 / 1.92 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.73 seconds wall clock time: 31 minutes 4.09 seconds (1864.09 seconds total)