Starting phenix.real_space_refine on Thu Aug 6 05:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.map" model { file = "/net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eil_48086/08_2026/9eil_48086.cif" } resolution = 3.2 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= -0.000 sd= 0.011 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 1 6.06 5 P 283 5.49 5 S 22 5.16 5 C 7951 2.51 5 N 2636 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14070 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2904 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain: "J" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2874 Classifications: {'DNA': 141} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 140} Chain: "K" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 270} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'ZSL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12877 SG CYS K 141 44.098 65.647 71.459 1.00114.38 S ATOM 12897 SG CYS K 144 43.190 68.486 69.603 1.00 89.70 S ATOM 13062 SG CYS K 166 41.380 64.971 68.847 1.00115.24 S ATOM 13140 SG CYS K 177 45.032 65.611 67.925 1.00101.68 S Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 14070 At special positions: 0 Unit cell: (111.22, 117.03, 127.82, 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 1 29.99 S 22 16.00 P 283 15.00 O 3177 8.00 N 2636 7.00 C 7951 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 298.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 177 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 144 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 166 " Number of angles added : 6 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 11 sheets defined 62.0% alpha, 4.4% beta 141 base pairs and 232 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.886A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.657A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.710A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.620A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.549A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.717A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.837A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.581A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.043A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.529A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.771A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 44 removed outlier: 3.879A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 4.154A pdb=" N SER K 59 " --> pdb=" O ILE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 76 Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.795A pdb=" N MET K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 125 through 129 Processing helix chain 'K' and resid 170 through 174 removed outlier: 4.332A pdb=" N GLY K 173 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 207 Processing helix chain 'K' and resid 224 through 231 removed outlier: 3.596A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.150A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.452A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.485A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.827A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.760A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 107 through 110 removed outlier: 6.664A pdb=" N VAL K 47 " --> pdb=" O ARG K 108 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU K 110 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE K 49 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL K 48 " --> pdb=" O ILE K 211 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU K 213 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N HIS K 50 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ILE K 254 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE K 238 " --> pdb=" O ILE K 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 147 through 149 removed outlier: 4.397A pdb=" N THR K 184 " --> pdb=" O ASN K 135 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 362 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 232 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3782 1.34 - 1.47: 4827 1.47 - 1.59: 5765 1.59 - 1.72: 486 1.72 - 1.85: 39 Bond restraints: 14899 Sorted by residual: bond pdb=" O39 ZSL A 201 " pdb=" P44 ZSL A 201 " ideal model delta sigma weight residual 1.497 1.398 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C3' DA I -53 " pdb=" O3' DA I -53 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C20 ZSL A 201 " pdb=" S46 ZSL A 201 " ideal model delta sigma weight residual 1.830 1.744 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C3' DG J 54 " pdb=" O3' DG J 54 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" C25 ZSL A 201 " pdb=" C27 ZSL A 201 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 14894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 21330 5.41 - 10.83: 16 10.83 - 16.24: 0 16.24 - 21.65: 1 21.65 - 27.07: 1 Bond angle restraints: 21348 Sorted by residual: angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP1 DG I 21 " ideal model delta sigma weight residual 108.00 80.93 27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP2 DG I 21 " ideal model delta sigma weight residual 108.00 87.51 20.49 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O4' DG I -5 " pdb=" C4' DG I -5 " pdb=" C3' DG I -5 " ideal model delta sigma weight residual 106.00 102.66 3.34 6.00e-01 2.78e+00 3.10e+01 angle pdb=" O4' DC I 61 " pdb=" C4' DC I 61 " pdb=" C3' DC I 61 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.44 5.09 9.80e-01 1.04e+00 2.70e+01 ... (remaining 21343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 6955 34.74 - 69.48: 1320 69.48 - 104.22: 16 104.22 - 138.95: 0 138.95 - 173.69: 2 Dihedral angle restraints: 8293 sinusoidal: 5272 harmonic: 3021 Sorted by residual: dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.69 -173.69 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 57.34 162.66 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA LYS C 75 " pdb=" CB LYS C 75 " pdb=" CG LYS C 75 " pdb=" CD LYS C 75 " ideal model delta sinusoidal sigma weight residual -180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.419: 2430 0.419 - 0.837: 0 0.837 - 1.256: 0 1.256 - 1.674: 0 1.674 - 2.093: 1 Chirality restraints: 2431 Sorted by residual: chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.34 0.24 2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" C PRO K 221 " pdb=" CB PRO K 221 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C18 ZSL A 201 " pdb=" C17 ZSL A 201 " pdb=" N07 ZSL A 201 " pdb=" O33 ZSL A 201 " both_signs ideal model delta sigma weight residual False 2.33 2.58 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2428 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 220 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO K 221 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -53 " 0.028 2.00e-02 2.50e+03 1.14e-02 3.59e+00 pdb=" N9 DA I -53 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DA I -53 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA I -53 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA I -53 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -53 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -53 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA I -53 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I -53 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA I -53 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DA I -53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " 0.024 2.00e-02 2.50e+03 1.09e-02 3.25e+00 pdb=" N9 DA I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " -0.003 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 526 2.70 - 3.25: 12942 3.25 - 3.80: 26513 3.80 - 4.35: 32702 4.35 - 4.90: 47691 Nonbonded interactions: 120374 Sorted by model distance: nonbonded pdb=" O SER K 56 " pdb=" OG SER K 59 " model vdw 2.151 3.040 nonbonded pdb=" O ARG K 220 " pdb=" N SER K 222 " model vdw 2.195 3.120 nonbonded pdb=" NH1 ARG D 83 " pdb=" OP2 DG I -33 " model vdw 2.195 3.120 nonbonded pdb=" OG1 THR B 80 " pdb=" O ARG E 83 " model vdw 2.224 3.040 nonbonded pdb=" NH2 ARG K 65 " pdb=" O37 ZSL A 201 " model vdw 2.232 3.120 ... (remaining 120369 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 14904 Z= 0.533 Angle : 0.798 27.067 21354 Z= 0.634 Chirality : 0.063 2.093 2431 Planarity : 0.005 0.111 1730 Dihedral : 25.585 173.694 6343 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.82 % Favored : 96.89 % Rotamer: Outliers : 2.19 % Allowed : 7.95 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.27), residues: 1028 helix: 2.68 (0.21), residues: 603 sheet: -1.98 (0.81), residues: 36 loop : -1.59 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.014 0.001 TYR K 5 PHE 0.009 0.001 PHE D 62 TRP 0.006 0.001 TRP K 71 HIS 0.003 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.53 (14899) covalent geometry : angle 0.78996 / 0.63 (21348) hydrogen bonds : bond 0.10677 / 7.15 ( 829) hydrogen bonds : angle 3.89888 / 2.75 ( 2098) metal coordination : bond 0.01166 / 0.58 ( 4) metal coordination : angle 6.66086 / 3.10 ( 6) Misc. bond : bond 0.07804 / 4.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 368 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.8664 (t80) cc_final: 0.8446 (t80) REVERT: C 92 GLU cc_start: 0.8007 (mp0) cc_final: 0.7254 (mp0) REVERT: E 45 THR cc_start: 0.8003 (t) cc_final: 0.7677 (p) REVERT: E 54 TYR cc_start: 0.8485 (m-80) cc_final: 0.8032 (m-80) REVERT: F 59 LYS cc_start: 0.8882 (ttpp) cc_final: 0.8645 (tttt) REVERT: G 38 ASN cc_start: 0.7955 (m-40) cc_final: 0.7137 (m-40) REVERT: G 77 ARG cc_start: 0.7285 (ptp-110) cc_final: 0.6956 (ptm160) REVERT: G 89 ASN cc_start: 0.8502 (m-40) cc_final: 0.8153 (m110) REVERT: K 95 HIS cc_start: 0.7935 (m90) cc_final: 0.7702 (m-70) REVERT: K 109 PHE cc_start: 0.8065 (t80) cc_final: 0.7641 (t80) outliers start: 19 outliers final: 3 residues processed: 381 average time/residue: 0.1529 time to fit residues: 77.0455 Evaluate side-chains 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain K residue 164 ARG Chi-restraints excluded: chain K residue 266 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 125 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN G 104 GLN H 60 ASN H 106 HIS ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN K 268 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.107241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067065 restraints weight = 44612.183| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.80 r_work: 0.2943 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 14904 Z= 0.201 Angle : 0.755 26.458 21354 Z= 0.417 Chirality : 0.061 1.983 2431 Planarity : 0.006 0.105 1730 Dihedral : 29.102 169.908 4313 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % Rotamer: Outliers : 5.07 % Allowed : 16.47 % Favored : 78.46 % 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: 1.22 (0.26), residues: 1028 helix: 2.33 (0.21), residues: 607 sheet: -1.68 (0.83), residues: 36 loop : -1.56 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 195 TYR 0.022 0.002 TYR B 88 PHE 0.025 0.002 PHE K 124 TRP 0.018 0.002 TRP K 276 HIS 0.010 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (14899) covalent geometry : angle 0.74969 / 0.42 (21348) hydrogen bonds : bond 0.05637 / 3.79 ( 829) hydrogen bonds : angle 3.43975 / 2.47 ( 2098) metal coordination : bond 0.01464 / 0.74 ( 4) metal coordination : angle 5.62293 / 2.77 ( 6) Misc. bond : bond 0.00854 / 0.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9493 (mt-10) cc_final: 0.9224 (tt0) REVERT: A 81 ASP cc_start: 0.8588 (m-30) cc_final: 0.8313 (p0) REVERT: B 93 GLN cc_start: 0.8865 (mt0) cc_final: 0.8527 (mp10) REVERT: E 60 LEU cc_start: 0.9371 (mt) cc_final: 0.9090 (mt) REVERT: F 59 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8494 (tttt) REVERT: G 38 ASN cc_start: 0.8094 (m-40) cc_final: 0.7888 (m-40) REVERT: G 92 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7542 (mt-10) REVERT: H 65 ASP cc_start: 0.9130 (t70) cc_final: 0.8900 (t0) REVERT: H 80 TYR cc_start: 0.8530 (m-10) cc_final: 0.7966 (m-10) REVERT: H 90 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7399 (mm-30) REVERT: H 102 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7946 (tm-30) REVERT: K 51 THR cc_start: 0.8905 (p) cc_final: 0.8518 (t) REVERT: K 101 LEU cc_start: 0.9445 (mt) cc_final: 0.9213 (mt) REVERT: K 109 PHE cc_start: 0.8803 (t80) cc_final: 0.8006 (t80) REVERT: K 113 GLN cc_start: 0.7558 (pm20) cc_final: 0.6989 (pm20) REVERT: K 131 GLU cc_start: 0.9180 (mp0) cc_final: 0.8916 (pm20) REVERT: K 147 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7612 (tm-30) REVERT: K 188 TRP cc_start: 0.8233 (m100) cc_final: 0.7867 (m100) REVERT: K 210 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7224 (p) REVERT: K 257 TYR cc_start: 0.9486 (m-80) cc_final: 0.9233 (t80) REVERT: K 265 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (mm) outliers start: 44 outliers final: 25 residues processed: 281 average time/residue: 0.1197 time to fit residues: 46.6187 Evaluate side-chains 257 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 90 ARG Chi-restraints excluded: chain K residue 164 ARG Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 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 = 0.4049 r_free = 0.4049 target = 0.107214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067309 restraints weight = 45063.388| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.83 r_work: 0.2933 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14904 Z= 0.173 Angle : 0.711 26.288 21354 Z= 0.395 Chirality : 0.060 2.013 2431 Planarity : 0.006 0.109 1730 Dihedral : 29.300 167.789 4310 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 4.72 % Allowed : 17.05 % Favored : 78.23 % 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: 1.24 (0.26), residues: 1028 helix: 2.30 (0.21), residues: 610 sheet: -1.58 (0.81), residues: 36 loop : -1.48 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 205 TYR 0.021 0.002 TYR D 80 PHE 0.012 0.001 PHE A 67 TRP 0.024 0.002 TRP K 276 HIS 0.014 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (14899) covalent geometry : angle 0.70772 / 0.39 (21348) hydrogen bonds : bond 0.05136 / 3.43 ( 829) hydrogen bonds : angle 3.26622 / 2.35 ( 2098) metal coordination : bond 0.01159 / 0.58 ( 4) metal coordination : angle 4.12855 / 2.10 ( 6) Misc. bond : bond 0.00601 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9265 (tt0) REVERT: B 93 GLN cc_start: 0.8815 (mt0) cc_final: 0.8583 (mp10) REVERT: C 89 ASN cc_start: 0.9307 (m-40) cc_final: 0.8961 (m110) REVERT: C 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8054 (t0) REVERT: C 91 GLU cc_start: 0.8539 (pm20) cc_final: 0.8229 (pm20) REVERT: C 92 GLU cc_start: 0.8739 (mp0) cc_final: 0.7791 (mp0) REVERT: E 60 LEU cc_start: 0.9347 (mt) cc_final: 0.9053 (mt) REVERT: F 59 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8503 (tttt) REVERT: F 88 TYR cc_start: 0.8691 (m-10) cc_final: 0.8274 (m-10) REVERT: G 38 ASN cc_start: 0.8206 (m-40) cc_final: 0.7807 (m-40) REVERT: G 91 GLU cc_start: 0.8816 (tt0) cc_final: 0.8473 (tp30) REVERT: H 65 ASP cc_start: 0.9183 (t70) cc_final: 0.8918 (t0) REVERT: H 76 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8042 (mtm-85) REVERT: H 80 TYR cc_start: 0.8440 (m-10) cc_final: 0.8048 (m-10) REVERT: H 90 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7415 (mm-30) REVERT: H 102 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7777 (tm-30) REVERT: K 17 LYS cc_start: 0.2982 (OUTLIER) cc_final: 0.1584 (pttt) REVERT: K 51 THR cc_start: 0.9156 (p) cc_final: 0.8605 (t) REVERT: K 95 HIS cc_start: 0.9116 (m90) cc_final: 0.8446 (m90) REVERT: K 109 PHE cc_start: 0.8826 (t80) cc_final: 0.7759 (t80) REVERT: K 113 GLN cc_start: 0.7544 (pm20) cc_final: 0.7104 (pm20) REVERT: K 147 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7630 (tm-30) REVERT: K 180 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8948 (pt0) REVERT: K 182 ARG cc_start: 0.9408 (mtt90) cc_final: 0.9048 (ptp-110) REVERT: K 188 TRP cc_start: 0.8242 (m100) cc_final: 0.7967 (m100) REVERT: K 196 ASP cc_start: 0.9234 (m-30) cc_final: 0.8356 (t0) REVERT: K 197 LEU cc_start: 0.8793 (mm) cc_final: 0.8141 (mm) REVERT: K 257 TYR cc_start: 0.9486 (m-80) cc_final: 0.9234 (t80) outliers start: 41 outliers final: 29 residues processed: 277 average time/residue: 0.1124 time to fit residues: 44.1044 Evaluate side-chains 259 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 90 ARG Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 50.0000 chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS H 60 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 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 = 0.4004 r_free = 0.4004 target = 0.103254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062753 restraints weight = 44916.415| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.79 r_work: 0.2854 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 14904 Z= 0.333 Angle : 0.804 26.541 21354 Z= 0.430 Chirality : 0.061 1.982 2431 Planarity : 0.006 0.110 1730 Dihedral : 29.644 165.996 4306 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 5.30 % Allowed : 19.01 % Favored : 75.69 % 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: 0.77 (0.26), residues: 1028 helix: 1.89 (0.20), residues: 618 sheet: -1.68 (0.82), residues: 36 loop : -1.71 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 121 TYR 0.023 0.002 TYR C 57 PHE 0.021 0.002 PHE A 67 TRP 0.056 0.004 TRP K 276 HIS 0.014 0.002 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.33 (14899) covalent geometry : angle 0.80090 / 0.43 (21348) hydrogen bonds : bond 0.06366 / 4.30 ( 829) hydrogen bonds : angle 3.53041 / 2.54 ( 2098) metal coordination : bond 0.02022 / 0.98 ( 4) metal coordination : angle 4.34434 / 2.46 ( 6) Misc. bond : bond 0.00137 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8816 (tp40) cc_final: 0.8611 (tp40) REVERT: B 88 TYR cc_start: 0.9069 (m-10) cc_final: 0.8369 (m-10) REVERT: B 93 GLN cc_start: 0.8925 (mt0) cc_final: 0.8718 (mp10) REVERT: C 90 ASP cc_start: 0.8621 (t70) cc_final: 0.8200 (t0) REVERT: C 91 GLU cc_start: 0.8598 (pm20) cc_final: 0.8096 (pm20) REVERT: C 92 GLU cc_start: 0.8738 (mp0) cc_final: 0.7740 (mp0) REVERT: E 94 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8362 (mm-30) REVERT: E 105 GLU cc_start: 0.8854 (tt0) cc_final: 0.8485 (mt-10) REVERT: E 122 LYS cc_start: 0.9055 (ptpt) cc_final: 0.8844 (pttt) REVERT: F 59 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8631 (tttt) REVERT: G 91 GLU cc_start: 0.8868 (tt0) cc_final: 0.8537 (tp30) REVERT: G 92 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7658 (mt-10) REVERT: H 65 ASP cc_start: 0.9284 (t70) cc_final: 0.9022 (t0) REVERT: H 80 TYR cc_start: 0.8413 (m-10) cc_final: 0.8026 (m-10) REVERT: H 102 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7963 (tm-30) REVERT: K 51 THR cc_start: 0.9157 (p) cc_final: 0.8582 (t) REVERT: K 55 ILE cc_start: 0.7563 (mm) cc_final: 0.7037 (mm) REVERT: K 95 HIS cc_start: 0.9054 (m90) cc_final: 0.8655 (m90) REVERT: K 109 PHE cc_start: 0.8830 (t80) cc_final: 0.7824 (t80) REVERT: K 113 GLN cc_start: 0.7804 (pm20) cc_final: 0.7508 (pm20) REVERT: K 131 GLU cc_start: 0.9222 (mp0) cc_final: 0.8765 (pm20) REVERT: K 188 TRP cc_start: 0.8316 (m100) cc_final: 0.8047 (m100) REVERT: K 196 ASP cc_start: 0.9294 (m-30) cc_final: 0.8436 (t0) REVERT: K 197 LEU cc_start: 0.8741 (mm) cc_final: 0.8464 (mm) REVERT: K 238 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7682 (pt) REVERT: K 257 TYR cc_start: 0.9497 (OUTLIER) cc_final: 0.9255 (t80) REVERT: K 266 MET cc_start: 0.8366 (ttp) cc_final: 0.8056 (ttm) outliers start: 46 outliers final: 34 residues processed: 253 average time/residue: 0.1170 time to fit residues: 42.4447 Evaluate side-chains 252 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 128 optimal weight: 0.0000 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 50.0000 chunk 105 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 79 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.105290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065516 restraints weight = 45028.785| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.75 r_work: 0.2921 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14904 Z= 0.154 Angle : 0.707 26.316 21354 Z= 0.388 Chirality : 0.060 2.024 2431 Planarity : 0.005 0.112 1730 Dihedral : 29.542 163.959 4306 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.82 % Favored : 96.89 % Rotamer: Outliers : 4.26 % Allowed : 20.62 % Favored : 75.12 % 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: 1.17 (0.26), residues: 1028 helix: 2.21 (0.21), residues: 618 sheet: -1.56 (0.86), residues: 36 loop : -1.55 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 76 TYR 0.022 0.002 TYR C 57 PHE 0.028 0.002 PHE K 124 TRP 0.036 0.003 TRP K 276 HIS 0.017 0.002 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (14899) covalent geometry : angle 0.70467 / 0.39 (21348) hydrogen bonds : bond 0.04744 / 3.14 ( 829) hydrogen bonds : angle 3.16706 / 2.29 ( 2098) metal coordination : bond 0.00914 / 0.45 ( 4) metal coordination : angle 3.50621 / 2.04 ( 6) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8936 (m-10) cc_final: 0.8676 (m-10) REVERT: C 41 GLU cc_start: 0.8402 (mp0) cc_final: 0.8176 (mp0) REVERT: C 90 ASP cc_start: 0.8593 (t70) cc_final: 0.8157 (t0) REVERT: C 91 GLU cc_start: 0.8628 (pm20) cc_final: 0.8136 (pm20) REVERT: C 92 GLU cc_start: 0.8746 (mp0) cc_final: 0.7696 (mp0) REVERT: E 60 LEU cc_start: 0.9308 (mt) cc_final: 0.9037 (mt) REVERT: E 105 GLU cc_start: 0.8807 (tt0) cc_final: 0.8397 (mt-10) REVERT: F 59 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8541 (tttt) REVERT: F 88 TYR cc_start: 0.8724 (m-10) cc_final: 0.8069 (m-10) REVERT: G 91 GLU cc_start: 0.8793 (tt0) cc_final: 0.8444 (tp30) REVERT: G 92 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7578 (mt-10) REVERT: H 65 ASP cc_start: 0.9232 (t70) cc_final: 0.8940 (t0) REVERT: H 80 TYR cc_start: 0.8295 (m-10) cc_final: 0.7826 (m-10) REVERT: H 102 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7931 (tm-30) REVERT: K 17 LYS cc_start: 0.2991 (OUTLIER) cc_final: 0.1168 (pttp) REVERT: K 51 THR cc_start: 0.9210 (p) cc_final: 0.8613 (t) REVERT: K 55 ILE cc_start: 0.7328 (mm) cc_final: 0.6912 (mm) REVERT: K 95 HIS cc_start: 0.9240 (m-70) cc_final: 0.8998 (m90) REVERT: K 109 PHE cc_start: 0.8781 (t80) cc_final: 0.7756 (t80) REVERT: K 113 GLN cc_start: 0.7842 (pm20) cc_final: 0.7536 (pm20) REVERT: K 131 GLU cc_start: 0.9180 (mp0) cc_final: 0.8604 (pm20) REVERT: K 196 ASP cc_start: 0.9274 (m-30) cc_final: 0.8409 (t0) REVERT: K 197 LEU cc_start: 0.8692 (mm) cc_final: 0.8415 (mm) REVERT: K 257 TYR cc_start: 0.9483 (OUTLIER) cc_final: 0.9244 (t80) outliers start: 37 outliers final: 28 residues processed: 260 average time/residue: 0.1225 time to fit residues: 45.2566 Evaluate side-chains 258 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 71 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 30.0000 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 108 optimal weight: 0.0070 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 95 HIS ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 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 = 0.4057 r_free = 0.4057 target = 0.106030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066273 restraints weight = 44812.992| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.80 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14904 Z= 0.146 Angle : 0.697 26.433 21354 Z= 0.382 Chirality : 0.059 2.010 2431 Planarity : 0.005 0.114 1730 Dihedral : 29.453 164.967 4306 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % Rotamer: Outliers : 3.34 % Allowed : 21.66 % Favored : 75.00 % 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: 1.30 (0.26), residues: 1028 helix: 2.34 (0.21), residues: 617 sheet: -1.51 (0.81), residues: 44 loop : -1.54 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.024 0.002 TYR E 54 PHE 0.020 0.002 PHE K 124 TRP 0.046 0.005 TRP K 276 HIS 0.012 0.001 HIS K 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (14899) covalent geometry : angle 0.69556 / 0.38 (21348) hydrogen bonds : bond 0.04606 / 3.06 ( 829) hydrogen bonds : angle 3.13012 / 2.25 ( 2098) metal coordination : bond 0.00797 / 0.39 ( 4) metal coordination : angle 3.13732 / 1.80 ( 6) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7785 (mp0) cc_final: 0.7522 (mp0) REVERT: C 90 ASP cc_start: 0.8445 (t70) cc_final: 0.7900 (t0) REVERT: C 91 GLU cc_start: 0.8371 (pm20) cc_final: 0.7662 (pm20) REVERT: C 92 GLU cc_start: 0.8452 (mp0) cc_final: 0.7352 (mp0) REVERT: E 60 LEU cc_start: 0.9233 (mt) cc_final: 0.8965 (mt) REVERT: E 105 GLU cc_start: 0.8167 (tt0) cc_final: 0.7783 (mt-10) REVERT: F 59 LYS cc_start: 0.8699 (ttpp) cc_final: 0.8322 (tttt) REVERT: F 88 TYR cc_start: 0.8258 (m-10) cc_final: 0.7636 (m-10) REVERT: G 91 GLU cc_start: 0.8420 (tt0) cc_final: 0.8204 (tp30) REVERT: G 92 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7418 (mt-10) REVERT: H 65 ASP cc_start: 0.8911 (t70) cc_final: 0.8591 (t0) REVERT: H 80 TYR cc_start: 0.8047 (m-10) cc_final: 0.7649 (m-10) REVERT: H 103 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (tp) REVERT: K 17 LYS cc_start: 0.2740 (OUTLIER) cc_final: 0.1442 (pttt) REVERT: K 51 THR cc_start: 0.9104 (p) cc_final: 0.8470 (t) REVERT: K 55 ILE cc_start: 0.7332 (mm) cc_final: 0.6825 (mm) REVERT: K 100 GLN cc_start: 0.9137 (tp40) cc_final: 0.8863 (mm-40) REVERT: K 109 PHE cc_start: 0.8691 (t80) cc_final: 0.7690 (t80) REVERT: K 113 GLN cc_start: 0.7853 (pm20) cc_final: 0.7568 (pm20) REVERT: K 196 ASP cc_start: 0.9268 (m-30) cc_final: 0.8428 (t0) REVERT: K 197 LEU cc_start: 0.8741 (mm) cc_final: 0.8466 (mm) REVERT: K 257 TYR cc_start: 0.9417 (OUTLIER) cc_final: 0.9176 (t80) outliers start: 29 outliers final: 24 residues processed: 263 average time/residue: 0.1096 time to fit residues: 41.0469 Evaluate side-chains 257 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 60 ASN ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.105761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066298 restraints weight = 45267.828| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.77 r_work: 0.2948 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14904 Z= 0.163 Angle : 0.700 26.446 21354 Z= 0.381 Chirality : 0.059 2.008 2431 Planarity : 0.005 0.116 1730 Dihedral : 29.463 165.768 4306 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.40 % Favored : 96.30 % Rotamer: Outliers : 3.92 % Allowed : 21.77 % Favored : 74.31 % 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: 1.28 (0.26), residues: 1028 helix: 2.35 (0.21), residues: 615 sheet: -1.61 (0.79), residues: 44 loop : -1.54 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.016 0.001 TYR C 57 PHE 0.023 0.002 PHE A 67 TRP 0.038 0.004 TRP K 188 HIS 0.022 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (14899) covalent geometry : angle 0.69811 / 0.38 (21348) hydrogen bonds : bond 0.04693 / 3.12 ( 829) hydrogen bonds : angle 3.15581 / 2.27 ( 2098) metal coordination : bond 0.00886 / 0.44 ( 4) metal coordination : angle 2.84316 / 1.64 ( 6) Misc. bond : bond 0.00104 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8874 (m-10) cc_final: 0.7912 (m-10) REVERT: B 93 GLN cc_start: 0.8669 (mp10) cc_final: 0.8196 (mp10) REVERT: C 90 ASP cc_start: 0.8693 (t70) cc_final: 0.8183 (t0) REVERT: C 91 GLU cc_start: 0.8685 (pm20) cc_final: 0.8066 (pm20) REVERT: C 92 GLU cc_start: 0.8803 (mp0) cc_final: 0.7774 (mp0) REVERT: E 105 GLU cc_start: 0.8796 (tt0) cc_final: 0.8396 (mt-10) REVERT: F 59 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8568 (tttt) REVERT: F 88 TYR cc_start: 0.8614 (m-10) cc_final: 0.8082 (m-10) REVERT: G 91 GLU cc_start: 0.8775 (tt0) cc_final: 0.8355 (tp30) REVERT: G 92 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7741 (mt-10) REVERT: H 65 ASP cc_start: 0.9206 (t70) cc_final: 0.8904 (t0) REVERT: H 80 TYR cc_start: 0.8256 (m-10) cc_final: 0.7872 (m-10) REVERT: K 17 LYS cc_start: 0.2853 (OUTLIER) cc_final: 0.1176 (pttt) REVERT: K 51 THR cc_start: 0.9201 (p) cc_final: 0.8637 (t) REVERT: K 55 ILE cc_start: 0.7303 (mm) cc_final: 0.6704 (mm) REVERT: K 109 PHE cc_start: 0.8769 (t80) cc_final: 0.7777 (t80) REVERT: K 133 HIS cc_start: 0.6903 (m90) cc_final: 0.6455 (m90) REVERT: K 147 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: K 188 TRP cc_start: 0.7267 (m100) cc_final: 0.6843 (m100) REVERT: K 257 TYR cc_start: 0.9493 (OUTLIER) cc_final: 0.9258 (t80) outliers start: 34 outliers final: 27 residues processed: 250 average time/residue: 0.1297 time to fit residues: 45.9440 Evaluate side-chains 251 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 147 GLN Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 10.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 255 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 = 0.4022 r_free = 0.4022 target = 0.104348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065179 restraints weight = 44423.438| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.73 r_work: 0.2868 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14904 Z= 0.253 Angle : 0.753 26.520 21354 Z= 0.406 Chirality : 0.060 1.999 2431 Planarity : 0.006 0.119 1730 Dihedral : 29.615 165.888 4306 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % Rotamer: Outliers : 4.26 % Allowed : 22.24 % Favored : 73.50 % 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: 1.11 (0.26), residues: 1028 helix: 2.24 (0.21), residues: 610 sheet: -1.19 (0.88), residues: 38 loop : -1.68 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 76 TYR 0.039 0.002 TYR D 80 PHE 0.021 0.002 PHE A 67 TRP 0.034 0.004 TRP K 276 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (14899) covalent geometry : angle 0.75147 / 0.41 (21348) hydrogen bonds : bond 0.05401 / 3.62 ( 829) hydrogen bonds : angle 3.32663 / 2.39 ( 2098) metal coordination : bond 0.01170 / 0.57 ( 4) metal coordination : angle 2.95374 / 1.66 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8852 (m-10) cc_final: 0.8050 (m-10) REVERT: B 93 GLN cc_start: 0.8741 (mp10) cc_final: 0.8411 (mp10) REVERT: C 90 ASP cc_start: 0.8708 (t70) cc_final: 0.8115 (t0) REVERT: C 91 GLU cc_start: 0.8668 (pm20) cc_final: 0.8053 (pm20) REVERT: C 92 GLU cc_start: 0.8828 (mp0) cc_final: 0.7752 (mp0) REVERT: D 80 TYR cc_start: 0.8370 (m-10) cc_final: 0.7353 (m-10) REVERT: E 94 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8386 (mm-30) REVERT: E 105 GLU cc_start: 0.8819 (tt0) cc_final: 0.8377 (mt-10) REVERT: F 59 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8587 (tttt) REVERT: F 88 TYR cc_start: 0.8701 (m-10) cc_final: 0.8098 (m-10) REVERT: G 91 GLU cc_start: 0.8786 (tt0) cc_final: 0.8459 (tp30) REVERT: H 65 ASP cc_start: 0.9299 (t70) cc_final: 0.9008 (t0) REVERT: H 80 TYR cc_start: 0.8312 (m-10) cc_final: 0.7898 (m-10) REVERT: K 17 LYS cc_start: 0.2550 (OUTLIER) cc_final: 0.0649 (pttp) REVERT: K 51 THR cc_start: 0.9114 (p) cc_final: 0.8642 (t) REVERT: K 55 ILE cc_start: 0.7298 (mm) cc_final: 0.6651 (mm) REVERT: K 109 PHE cc_start: 0.8760 (t80) cc_final: 0.7798 (t80) REVERT: K 113 GLN cc_start: 0.7976 (pm20) cc_final: 0.7352 (pm20) REVERT: K 133 HIS cc_start: 0.6614 (m90) cc_final: 0.6044 (m90) REVERT: K 188 TRP cc_start: 0.7372 (m100) cc_final: 0.6970 (m100) REVERT: K 196 ASP cc_start: 0.9273 (m-30) cc_final: 0.8441 (t0) REVERT: K 197 LEU cc_start: 0.8523 (mm) cc_final: 0.8219 (mm) REVERT: K 257 TYR cc_start: 0.9488 (OUTLIER) cc_final: 0.9273 (t80) outliers start: 37 outliers final: 31 residues processed: 249 average time/residue: 0.1294 time to fit residues: 45.7784 Evaluate side-chains 253 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 147 GLN Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 116 optimal weight: 0.0050 chunk 110 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 147 GLN K 255 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.105794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066124 restraints weight = 44415.376| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.84 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14904 Z= 0.145 Angle : 0.700 26.406 21354 Z= 0.382 Chirality : 0.058 2.018 2431 Planarity : 0.005 0.119 1730 Dihedral : 29.460 164.828 4306 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 3.57 % Allowed : 23.96 % Favored : 72.47 % 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: 1.25 (0.26), residues: 1028 helix: 2.32 (0.21), residues: 617 sheet: -1.07 (0.87), residues: 38 loop : -1.64 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 30 TYR 0.013 0.002 TYR D 80 PHE 0.014 0.002 PHE K 124 TRP 0.032 0.004 TRP K 276 HIS 0.020 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (14899) covalent geometry : angle 0.69901 / 0.38 (21348) hydrogen bonds : bond 0.04541 / 3.00 ( 829) hydrogen bonds : angle 3.15963 / 2.27 ( 2098) metal coordination : bond 0.00544 / 0.27 ( 4) metal coordination : angle 2.59393 / 1.57 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8324 (m-10) cc_final: 0.7620 (m-10) REVERT: B 93 GLN cc_start: 0.8561 (mp10) cc_final: 0.8149 (mp10) REVERT: C 90 ASP cc_start: 0.8490 (t70) cc_final: 0.7799 (t0) REVERT: C 91 GLU cc_start: 0.8395 (pm20) cc_final: 0.7645 (pm20) REVERT: C 92 GLU cc_start: 0.8473 (mp0) cc_final: 0.7338 (mp0) REVERT: D 80 TYR cc_start: 0.8110 (m-10) cc_final: 0.7134 (m-10) REVERT: E 105 GLU cc_start: 0.8170 (tt0) cc_final: 0.7706 (mt-10) REVERT: F 59 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8274 (tttt) REVERT: F 88 TYR cc_start: 0.8286 (m-10) cc_final: 0.7538 (m-10) REVERT: G 91 GLU cc_start: 0.8420 (tt0) cc_final: 0.8209 (tp30) REVERT: H 65 ASP cc_start: 0.8956 (t70) cc_final: 0.8623 (t0) REVERT: H 80 TYR cc_start: 0.8070 (m-10) cc_final: 0.7626 (m-10) REVERT: K 17 LYS cc_start: 0.2484 (OUTLIER) cc_final: 0.1021 (pttt) REVERT: K 51 THR cc_start: 0.9054 (p) cc_final: 0.8559 (t) REVERT: K 55 ILE cc_start: 0.7332 (mm) cc_final: 0.6739 (mm) REVERT: K 109 PHE cc_start: 0.8692 (t80) cc_final: 0.7770 (t80) REVERT: K 113 GLN cc_start: 0.7867 (pm20) cc_final: 0.7435 (pm20) REVERT: K 188 TRP cc_start: 0.7437 (m100) cc_final: 0.6799 (m100) REVERT: K 196 ASP cc_start: 0.9255 (m-30) cc_final: 0.8402 (t0) REVERT: K 197 LEU cc_start: 0.8479 (mm) cc_final: 0.8187 (mm) REVERT: K 257 TYR cc_start: 0.9439 (OUTLIER) cc_final: 0.9227 (t80) outliers start: 31 outliers final: 25 residues processed: 256 average time/residue: 0.1289 time to fit residues: 47.0539 Evaluate side-chains 254 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 257 TYR Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.104491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065290 restraints weight = 44664.411| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.77 r_work: 0.2868 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 14904 Z= 0.219 Angle : 0.741 26.549 21354 Z= 0.397 Chirality : 0.059 1.998 2431 Planarity : 0.006 0.120 1730 Dihedral : 29.555 167.163 4306 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.40 % Favored : 96.40 % Rotamer: Outliers : 3.69 % Allowed : 23.50 % Favored : 72.81 % 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: 1.14 (0.26), residues: 1028 helix: 2.22 (0.21), residues: 617 sheet: -1.39 (0.79), residues: 43 loop : -1.63 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.025 0.002 TYR D 80 PHE 0.018 0.002 PHE A 67 TRP 0.031 0.004 TRP K 276 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (14899) covalent geometry : angle 0.73963 / 0.40 (21348) hydrogen bonds : bond 0.05206 / 3.50 ( 829) hydrogen bonds : angle 3.30764 / 2.38 ( 2098) metal coordination : bond 0.01163 / 0.57 ( 4) metal coordination : angle 2.69778 / 1.52 ( 6) Misc. bond : bond 0.00112 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8784 (m-10) cc_final: 0.8580 (m-10) REVERT: B 93 GLN cc_start: 0.8725 (mp10) cc_final: 0.8392 (mp10) REVERT: C 90 ASP cc_start: 0.8707 (t70) cc_final: 0.8417 (t0) REVERT: C 91 GLU cc_start: 0.8701 (pm20) cc_final: 0.8170 (pm20) REVERT: C 92 GLU cc_start: 0.8814 (mp0) cc_final: 0.8009 (mp0) REVERT: F 59 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8545 (tttt) REVERT: F 88 TYR cc_start: 0.8678 (m-10) cc_final: 0.8004 (m-10) REVERT: G 91 GLU cc_start: 0.8818 (tt0) cc_final: 0.8451 (tp30) REVERT: H 65 ASP cc_start: 0.9305 (t70) cc_final: 0.9004 (t0) REVERT: H 80 TYR cc_start: 0.8299 (m-10) cc_final: 0.7779 (m-10) REVERT: K 17 LYS cc_start: 0.2630 (OUTLIER) cc_final: 0.0674 (pttp) REVERT: K 51 THR cc_start: 0.9155 (p) cc_final: 0.8700 (t) REVERT: K 55 ILE cc_start: 0.7336 (mm) cc_final: 0.6720 (mm) REVERT: K 109 PHE cc_start: 0.8676 (t80) cc_final: 0.7845 (t80) REVERT: K 113 GLN cc_start: 0.8000 (pm20) cc_final: 0.7429 (pm20) REVERT: K 133 HIS cc_start: 0.6612 (m90) cc_final: 0.6113 (m90) REVERT: K 188 TRP cc_start: 0.7604 (m100) cc_final: 0.7091 (m100) REVERT: K 196 ASP cc_start: 0.9265 (m-30) cc_final: 0.8447 (t0) REVERT: K 197 LEU cc_start: 0.8463 (mm) cc_final: 0.8144 (mm) outliers start: 32 outliers final: 25 residues processed: 243 average time/residue: 0.1315 time to fit residues: 45.5734 Evaluate side-chains 247 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 276 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 40.0000 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** K 119 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 = 0.4026 r_free = 0.4026 target = 0.104506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064647 restraints weight = 44373.236| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.78 r_work: 0.2878 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 14904 Z= 0.186 Angle : 0.722 26.434 21354 Z= 0.388 Chirality : 0.059 2.012 2431 Planarity : 0.006 0.121 1730 Dihedral : 29.561 167.241 4306 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.02 % Favored : 96.79 % Rotamer: Outliers : 3.00 % Allowed : 24.65 % Favored : 72.35 % 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: 1.21 (0.26), residues: 1028 helix: 2.29 (0.21), residues: 610 sheet: -1.30 (0.79), residues: 43 loop : -1.55 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 76 TYR 0.019 0.002 TYR D 80 PHE 0.014 0.002 PHE A 67 TRP 0.031 0.003 TRP K 276 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (14899) covalent geometry : angle 0.72113 / 0.39 (21348) hydrogen bonds : bond 0.04805 / 3.21 ( 829) hydrogen bonds : angle 3.25528 / 2.34 ( 2098) metal coordination : bond 0.00967 / 0.48 ( 4) metal coordination : angle 2.56320 / 1.47 ( 6) Misc. bond : bond 0.00088 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.77 seconds wall clock time: 60 minutes 29.28 seconds (3629.28 seconds total)