Starting phenix.real_space_refine on Wed Feb 12 01:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3f_13179/02_2025/7p3f_13179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3f_13179/02_2025/7p3f_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_13179/02_2025/7p3f_13179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3f_13179/02_2025/7p3f_13179.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3f_13179/02_2025/7p3f_13179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3f_13179/02_2025/7p3f_13179_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.83, per 1000 atoms: 0.85 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 746.4 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: 2.78 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: 2.03 Time building geometry restraints manager: 2.18 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: 687 56.36 - 84.53: 114 84.53 - 112.71: 5 112.71 - 140.89: 2 Dihedral angle restraints: 4222 sinusoidal: 2518 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 4219 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: 2.210 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- 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 : 0.009 0.077 7202 Z= 0.572 Angle : 1.318 10.312 10226 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.013 0.003 HIS B 103 PHE 0.043 0.004 PHE B 38 TYR 0.011 0.002 TYR B 121 ARG 0.008 0.001 ARG C 36 *********************** 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 : 0.617 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: 0.2793 time to fit residues: 45.3539 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 : 0.812 ------------------------------------------------------------------------------- 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 55 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.197863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134883 restraints weight = 8165.085| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.82 r_work: 0.3381 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7202 Z= 0.208 Angle : 0.590 4.484 10226 Z= 0.350 Chirality : 0.037 0.169 1156 Planarity : 0.005 0.046 940 Dihedral : 28.424 138.508 2012 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 12.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.35), residues: 580 helix: 0.43 (0.32), residues: 270 sheet: -1.33 (0.50), residues: 104 loop : -1.02 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 103 PHE 0.010 0.001 PHE A 124 TYR 0.015 0.002 TYR B 121 ARG 0.004 0.000 ARG A 28 *********************** 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 109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.601 Fit side-chains REVERT: A 28 ARG cc_start: 0.9031 (tpt90) cc_final: 0.8791 (tpt90) REVERT: A 42 GLU cc_start: 0.7739 (pt0) cc_final: 0.7321 (pt0) REVERT: C 28 ARG cc_start: 0.9049 (tpt90) cc_final: 0.8802 (tpt90) REVERT: C 42 GLU cc_start: 0.7727 (pt0) cc_final: 0.7470 (pt0) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.2758 time to fit residues: 36.7558 Evaluate side-chains 95 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.198523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133175 restraints weight = 8096.783| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.36 r_work: 0.3327 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7202 Z= 0.181 Angle : 0.538 4.128 10226 Z= 0.318 Chirality : 0.037 0.233 1156 Planarity : 0.004 0.044 940 Dihedral : 27.677 146.067 2010 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 16.67 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.35), residues: 580 helix: 0.61 (0.32), residues: 272 sheet: -0.62 (0.51), residues: 104 loop : -1.28 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 8 PHE 0.011 0.001 PHE A 124 TYR 0.009 0.002 TYR D 121 ARG 0.003 0.000 ARG B 12 *********************** 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 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7905 (mmt180) cc_final: 0.6582 (ttp-110) REVERT: A 28 ARG cc_start: 0.8914 (tpt90) cc_final: 0.8383 (tpt90) REVERT: A 42 GLU cc_start: 0.7705 (pt0) cc_final: 0.7299 (pt0) REVERT: C 17 ARG cc_start: 0.8053 (mmt180) cc_final: 0.6828 (ttp-110) REVERT: C 28 ARG cc_start: 0.8963 (tpt90) cc_final: 0.8399 (tpt90) REVERT: C 42 GLU cc_start: 0.7770 (pt0) cc_final: 0.7480 (pt0) REVERT: B 30 GLN cc_start: 0.7816 (tt0) cc_final: 0.7118 (tt0) REVERT: D 26 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7386 (ttt180) REVERT: D 30 GLN cc_start: 0.7842 (tt0) cc_final: 0.7144 (tt0) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 0.2877 time to fit residues: 41.5784 Evaluate side-chains 102 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain B residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.193812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130020 restraints weight = 8228.953| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.16 r_work: 0.3240 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7202 Z= 0.313 Angle : 0.591 5.514 10226 Z= 0.338 Chirality : 0.037 0.135 1156 Planarity : 0.005 0.046 940 Dihedral : 28.086 142.599 2010 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.36), residues: 580 helix: 0.26 (0.32), residues: 276 sheet: -0.73 (0.51), residues: 104 loop : -0.87 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.016 0.002 PHE A 124 TYR 0.010 0.002 TYR B 121 ARG 0.005 0.000 ARG D 123 *********************** 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 123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8110 (mmt180) cc_final: 0.6781 (ttp-110) REVERT: A 28 ARG cc_start: 0.8936 (tpt90) cc_final: 0.8302 (tpt90) REVERT: A 42 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: C 17 ARG cc_start: 0.8144 (mmt180) cc_final: 0.6941 (ttp-110) REVERT: C 28 ARG cc_start: 0.8963 (tpt90) cc_final: 0.8293 (tpt90) REVERT: D 30 GLN cc_start: 0.7854 (tt0) cc_final: 0.7161 (tt0) outliers start: 17 outliers final: 15 residues processed: 112 average time/residue: 0.2601 time to fit residues: 36.0289 Evaluate side-chains 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 42 GLU Chi-restraints excluded: chain A residue 52 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 126 SER Chi-restraints excluded: chain B residue 24 SER 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 Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.197079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131476 restraints weight = 8050.595| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.57 r_work: 0.3275 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.003 0.027 7202 Z= 0.202 Angle : 0.527 5.535 10226 Z= 0.307 Chirality : 0.034 0.131 1156 Planarity : 0.004 0.044 940 Dihedral : 27.667 145.491 2010 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.37 % Allowed : 16.67 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.36), residues: 580 helix: 0.43 (0.33), residues: 272 sheet: 0.08 (0.53), residues: 94 loop : -0.93 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.010 0.001 PHE A 124 TYR 0.009 0.002 TYR D 121 ARG 0.002 0.000 ARG D 123 *********************** 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 123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8948 (tpt90) cc_final: 0.8459 (tpt-90) REVERT: A 42 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: C 42 GLU cc_start: 0.7494 (pt0) cc_final: 0.7195 (pt0) REVERT: B 23 THR cc_start: 0.7684 (p) cc_final: 0.7417 (t) REVERT: B 30 GLN cc_start: 0.7767 (tt0) cc_final: 0.7314 (tt0) REVERT: D 23 THR cc_start: 0.7666 (p) cc_final: 0.7408 (t) REVERT: D 30 GLN cc_start: 0.7845 (tt0) cc_final: 0.7375 (tt0) outliers start: 17 outliers final: 12 residues processed: 114 average time/residue: 0.2392 time to fit residues: 34.5072 Evaluate side-chains 115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 126 SER 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 24 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.199152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133381 restraints weight = 8242.995| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.63 r_work: 0.3302 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7202 Z= 0.164 Angle : 0.514 5.589 10226 Z= 0.299 Chirality : 0.033 0.130 1156 Planarity : 0.004 0.043 940 Dihedral : 27.299 145.276 2010 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.36), residues: 580 helix: 0.74 (0.33), residues: 272 sheet: -0.31 (0.52), residues: 104 loop : -0.67 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.008 0.001 PHE B 137 TYR 0.008 0.001 TYR B 121 ARG 0.002 0.000 ARG D 123 *********************** 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 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8946 (tpt90) cc_final: 0.8475 (tpt-90) REVERT: A 42 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: C 7 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7693 (mmm-85) REVERT: C 28 ARG cc_start: 0.8988 (tpt90) cc_final: 0.8525 (tpt90) REVERT: B 23 THR cc_start: 0.7635 (p) cc_final: 0.7392 (t) REVERT: B 30 GLN cc_start: 0.7758 (tt0) cc_final: 0.7364 (tt0) REVERT: D 23 THR cc_start: 0.7587 (p) cc_final: 0.7359 (t) REVERT: D 30 GLN cc_start: 0.7824 (tt0) cc_final: 0.7435 (tt0) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.2429 time to fit residues: 32.6677 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 : 0.748 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 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 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 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 72 GLN D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.196753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131566 restraints weight = 8105.913| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.87 r_work: 0.3239 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7202 Z= 0.216 Angle : 0.527 5.726 10226 Z= 0.304 Chirality : 0.034 0.128 1156 Planarity : 0.004 0.044 940 Dihedral : 27.334 145.058 2010 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.78 % Allowed : 18.65 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.36), residues: 580 helix: 0.72 (0.32), residues: 276 sheet: -0.27 (0.52), residues: 104 loop : -0.72 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 8 PHE 0.012 0.001 PHE A 124 TYR 0.006 0.001 TYR B 121 ARG 0.003 0.000 ARG D 123 *********************** 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 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8983 (tpt90) cc_final: 0.8497 (tpt-90) REVERT: A 42 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: C 28 ARG cc_start: 0.9001 (tpt90) cc_final: 0.8693 (tpt90) REVERT: B 23 THR cc_start: 0.7605 (p) cc_final: 0.7360 (t) REVERT: B 30 GLN cc_start: 0.7776 (tt0) cc_final: 0.7376 (tt0) REVERT: D 30 GLN cc_start: 0.7816 (tt0) cc_final: 0.7431 (tt0) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.2607 time to fit residues: 33.3253 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 : 0.593 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 GLU 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 44 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** 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 = 0.4338 r_free = 0.4338 target = 0.195962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130275 restraints weight = 8155.883| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.87 r_work: 0.3231 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7202 Z= 0.248 Angle : 0.541 6.390 10226 Z= 0.309 Chirality : 0.034 0.129 1156 Planarity : 0.004 0.045 940 Dihedral : 27.333 144.810 2010 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.37 % Allowed : 18.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.36), residues: 580 helix: 0.66 (0.32), residues: 276 sheet: -0.31 (0.52), residues: 104 loop : -0.66 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 8 PHE 0.013 0.002 PHE A 124 TYR 0.007 0.002 TYR B 121 ARG 0.004 0.000 ARG C 7 *********************** 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 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8994 (tpt90) cc_final: 0.8639 (tpt-90) REVERT: A 42 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: C 7 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7621 (tpp-160) REVERT: C 28 ARG cc_start: 0.8992 (tpt90) cc_final: 0.8556 (tpt-90) REVERT: B 23 THR cc_start: 0.7691 (p) cc_final: 0.7436 (t) REVERT: B 30 GLN cc_start: 0.7812 (tt0) cc_final: 0.7420 (tt0) REVERT: D 23 THR cc_start: 0.7608 (p) cc_final: 0.7368 (t) REVERT: D 30 GLN cc_start: 0.7831 (tt0) cc_final: 0.7453 (tt0) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.2465 time to fit residues: 33.0695 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 : 0.633 ------------------------------------------------------------------------------- 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 42 GLU 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 52 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 138 GLU 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 44 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** 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 = 0.4324 r_free = 0.4324 target = 0.194680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128180 restraints weight = 8240.091| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.81 r_work: 0.3205 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7202 Z= 0.299 Angle : 0.567 6.849 10226 Z= 0.322 Chirality : 0.035 0.127 1156 Planarity : 0.005 0.045 940 Dihedral : 27.403 144.430 2010 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.17 % Allowed : 18.25 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.36), residues: 580 helix: 0.48 (0.31), residues: 276 sheet: -0.43 (0.51), residues: 104 loop : -0.60 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 8 PHE 0.015 0.002 PHE A 124 TYR 0.007 0.002 TYR B 121 ARG 0.006 0.000 ARG A 27 *********************** 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 109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.9020 (tpt90) cc_final: 0.8584 (tpt90) REVERT: A 42 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: C 28 ARG cc_start: 0.8998 (tpt90) cc_final: 0.8301 (tpt90) REVERT: B 30 GLN cc_start: 0.7810 (tt0) cc_final: 0.7402 (tt0) REVERT: D 30 GLN cc_start: 0.7840 (tt0) cc_final: 0.7437 (tt0) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.2591 time to fit residues: 32.2859 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 42 GLU Chi-restraints excluded: chain A residue 52 SER 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 126 SER Chi-restraints excluded: chain C residue 138 GLU 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 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.0030 chunk 65 optimal weight: 8.9990 overall best weight: 0.4468 ------------------------------------------------------------------------------- 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 ** 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 = 0.4305 r_free = 0.4305 target = 0.194648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130955 restraints weight = 8400.889| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.68 r_work: 0.3246 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7202 Z= 0.157 Angle : 0.517 8.186 10226 Z= 0.298 Chirality : 0.033 0.126 1156 Planarity : 0.004 0.043 940 Dihedral : 26.983 143.617 2010 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.18 % Allowed : 18.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.35), residues: 580 helix: 0.79 (0.32), residues: 276 sheet: 0.30 (0.53), residues: 94 loop : -0.85 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 8 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR B 121 ARG 0.004 0.000 ARG C 7 ********************** 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: 11 poor density : 102 time to evaluate : 1.225 Fit side-chains REVERT: A 28 ARG cc_start: 0.8976 (tpt90) cc_final: 0.8460 (tpt90) REVERT: A 42 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: C 28 ARG cc_start: 0.8984 (tpt90) cc_final: 0.8585 (tpt90) REVERT: C 30 GLN cc_start: 0.8215 (tt0) cc_final: 0.7610 (tm-30) REVERT: C 42 GLU cc_start: 0.7335 (pt0) cc_final: 0.7006 (pt0) REVERT: B 23 THR cc_start: 0.7528 (p) cc_final: 0.7300 (t) REVERT: B 30 GLN cc_start: 0.7697 (tt0) cc_final: 0.7299 (tt0) REVERT: D 23 THR cc_start: 0.7543 (p) cc_final: 0.7331 (t) REVERT: D 30 GLN cc_start: 0.7719 (tt0) cc_final: 0.7371 (tt0) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.2479 time to fit residues: 32.4944 Evaluate side-chains 108 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 C residue 25 ILE Chi-restraints excluded: chain C residue 40 THR 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 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.1244 ------------------------------------------------------------------------------- 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 ** 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 = 0.4351 r_free = 0.4351 target = 0.196933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131420 restraints weight = 8373.044| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.69 r_work: 0.3261 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7202 Z= 0.227 Angle : 0.544 7.437 10226 Z= 0.310 Chirality : 0.034 0.139 1156 Planarity : 0.004 0.043 940 Dihedral : 27.103 143.639 2010 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.18 % Allowed : 18.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.36), residues: 580 helix: 0.63 (0.32), residues: 276 sheet: -0.30 (0.52), residues: 104 loop : -0.49 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 8 PHE 0.012 0.001 PHE A 124 TYR 0.008 0.001 TYR B 121 ARG 0.004 0.000 ARG C 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.57 seconds wall clock time: 66 minutes 54.72 seconds (4014.72 seconds total)