Starting phenix.real_space_refine on Fri Jul 3 10:53:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eil_48086/07_2026/9eil_48086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eil_48086/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2026/9eil_48086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2026/9eil_48086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2026/9eil_48086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eil_48086/07_2026/9eil_48086.map" } 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-dev-6108/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: 2.65, per 1000 atoms: 0.19 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 375.4 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: 1.66 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: 2.93 Time building geometry restraints manager: 1.33 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.290 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.900 ------------------------------------------------------------------------------- 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 : 0.793 27.067 21354 Z= 0.630 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 0.78491 / 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 : 0.301 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: 0.7255 (mp0) REVERT: E 45 THR cc_start: 0.8003 (t) cc_final: 0.7682 (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: 0.6957 (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: 0.7642 (t80) outliers start: 19 outliers final: 3 residues processed: 381 average time/residue: 0.1559 time to fit residues: 78.0548 Evaluate side-chains 255 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.4055 r_free = 0.4055 target = 0.107334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067569 restraints weight = 45162.921| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.78 r_work: 0.2941 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14904 Z= 0.201 Angle : 0.743 27.369 21354 Z= 0.413 Chirality : 0.061 2.059 2431 Planarity : 0.006 0.105 1730 Dihedral : 29.196 169.467 4313 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 5.18 % Allowed : 16.24 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.26), residues: 1028 helix: 2.29 (0.21), residues: 610 sheet: -1.67 (0.83), residues: 36 loop : -1.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 195 TYR 0.019 0.002 TYR B 88 PHE 0.025 0.001 PHE K 124 TRP 0.015 0.002 TRP K 276 HIS 0.010 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (14899) covalent geometry : angle 0.73709 / 0.41 (21348) hydrogen bonds : bond 0.05664 / 3.80 ( 829) hydrogen bonds : angle 3.42728 / 2.46 ( 2098) metal coordination : bond 0.01457 / 0.73 ( 4) metal coordination : angle 5.56885 / 2.73 ( 6) Misc. bond : bond 0.00844 / 0.44 ( 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: 45 poor density : 248 time to evaluate : 0.383 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: 0.9490 (mt-10) cc_final: 0.9226 (tt0) REVERT: A 81 ASP cc_start: 0.8593 (m-30) cc_final: 0.8312 (p0) REVERT: A 90 MET cc_start: 0.9165 (mmm) cc_final: 0.8800 (mmp) REVERT: B 93 GLN cc_start: 0.8859 (mt0) cc_final: 0.8525 (mp10) REVERT: E 45 THR cc_start: 0.8010 (t) cc_final: 0.7634 (p) REVERT: E 60 LEU cc_start: 0.9371 (mt) cc_final: 0.9090 (mt) REVERT: F 59 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8489 (tttt) REVERT: G 38 ASN cc_start: 0.8110 (m-40) cc_final: 0.7903 (m-40) REVERT: G 92 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7564 (mt-10) REVERT: H 65 ASP cc_start: 0.9132 (t70) cc_final: 0.8896 (t0) REVERT: H 80 TYR cc_start: 0.8527 (m-10) cc_final: 0.7928 (m-10) REVERT: H 102 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7943 (tm-30) REVERT: K 51 THR cc_start: 0.8912 (p) cc_final: 0.8524 (t) REVERT: K 101 LEU cc_start: 0.9448 (mt) cc_final: 0.9216 (mt) REVERT: K 109 PHE cc_start: 0.8807 (t80) cc_final: 0.8011 (t80) REVERT: K 113 GLN cc_start: 0.7649 (pm20) cc_final: 0.7099 (pm20) REVERT: K 131 GLU cc_start: 0.9172 (mp0) cc_final: 0.8912 (pm20) REVERT: K 147 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7611 (tm-30) REVERT: K 188 TRP cc_start: 0.8228 (m100) cc_final: 0.7867 (m100) REVERT: K 210 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7149 (p) REVERT: K 257 TYR cc_start: 0.9487 (m-80) cc_final: 0.9234 (t80) REVERT: K 265 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8479 (mm) outliers start: 45 outliers final: 23 residues processed: 280 average time/residue: 0.1326 time to fit residues: 51.0496 Evaluate side-chains 253 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 83 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 97 optimal weight: 10.9990 chunk 84 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066768 restraints weight = 45244.797| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.83 r_work: 0.2917 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 14904 Z= 0.199 Angle : 0.718 27.158 21354 Z= 0.399 Chirality : 0.060 2.070 2431 Planarity : 0.006 0.107 1730 Dihedral : 29.417 167.218 4310 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.21 % Favored : 96.50 % Rotamer: Outliers : 4.72 % Allowed : 17.40 % Favored : 77.88 % 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: 1.16 (0.26), residues: 1028 helix: 2.27 (0.21), residues: 610 sheet: -2.05 (0.72), residues: 43 loop : -1.50 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 205 TYR 0.024 0.002 TYR D 80 PHE 0.012 0.001 PHE A 67 TRP 0.020 0.002 TRP K 276 HIS 0.018 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (14899) covalent geometry : angle 0.71487 / 0.40 (21348) hydrogen bonds : bond 0.05300 / 3.55 ( 829) hydrogen bonds : angle 3.33556 / 2.40 ( 2098) metal coordination : bond 0.01253 / 0.63 ( 4) metal coordination : angle 4.33887 / 2.20 ( 6) Misc. bond : bond 0.00588 / 0.31 ( 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 277 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9276 (tt0) REVERT: E 45 THR cc_start: 0.8039 (t) cc_final: 0.7702 (p) REVERT: E 60 LEU cc_start: 0.9345 (mt) cc_final: 0.9041 (mt) REVERT: F 59 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8523 (tttt) REVERT: F 88 TYR cc_start: 0.8670 (m-10) cc_final: 0.8233 (m-10) REVERT: G 38 ASN cc_start: 0.8236 (m-40) cc_final: 0.7850 (m-40) REVERT: G 91 GLU cc_start: 0.8824 (tt0) cc_final: 0.8486 (tp30) REVERT: H 65 ASP cc_start: 0.9206 (t70) cc_final: 0.8949 (t0) REVERT: H 76 ARG cc_start: 0.8289 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: H 80 TYR cc_start: 0.8435 (m-10) cc_final: 0.8057 (m-10) REVERT: H 102 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7787 (tm-30) REVERT: K 51 THR cc_start: 0.9151 (p) cc_final: 0.8627 (t) REVERT: K 95 HIS cc_start: 0.9111 (m90) cc_final: 0.8490 (m90) REVERT: K 109 PHE cc_start: 0.8823 (t80) cc_final: 0.7752 (t80) REVERT: K 113 GLN cc_start: 0.7522 (pm20) cc_final: 0.7064 (pm20) REVERT: K 147 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7633 (tm-30) REVERT: K 180 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8908 (pt0) REVERT: K 182 ARG cc_start: 0.9410 (mtt90) cc_final: 0.8830 (ttm110) REVERT: K 196 ASP cc_start: 0.9245 (m-30) cc_final: 0.8366 (t0) REVERT: K 197 LEU cc_start: 0.8832 (mm) cc_final: 0.8523 (mm) REVERT: K 257 TYR cc_start: 0.9495 (m-80) cc_final: 0.9244 (t80) outliers start: 41 outliers final: 30 residues processed: 262 average time/residue: 0.1250 time to fit residues: 45.7875 Evaluate side-chains 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 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 87 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE 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 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 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 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: 0.7980 chunk 126 optimal weight: 1.9990 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: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.104791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.065112 restraints weight = 44954.772| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.82 r_work: 0.2872 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14904 Z= 0.261 Angle : 0.760 27.284 21354 Z= 0.412 Chirality : 0.061 2.060 2431 Planarity : 0.006 0.110 1730 Dihedral : 29.647 165.302 4306 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Rotamer: Outliers : 4.61 % Allowed : 18.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1028 helix: 2.11 (0.20), residues: 618 sheet: -1.66 (0.82), residues: 36 loop : -1.69 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 232 TYR 0.021 0.002 TYR C 57 PHE 0.015 0.002 PHE K 124 TRP 0.047 0.005 TRP K 276 HIS 0.011 0.001 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 (14899) covalent geometry : angle 0.75632 / 0.41 (21348) hydrogen bonds : bond 0.05618 / 3.78 ( 829) hydrogen bonds : angle 3.41208 / 2.46 ( 2098) metal coordination : bond 0.01643 / 0.81 ( 4) metal coordination : angle 4.28994 / 2.45 ( 6) Misc. bond : bond 0.00143 / 0.08 ( 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 271 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9282 (tt0) REVERT: B 93 GLN cc_start: 0.8707 (mp10) cc_final: 0.8399 (mp10) REVERT: C 41 GLU cc_start: 0.8443 (mp0) cc_final: 0.8233 (mp0) REVERT: E 45 THR cc_start: 0.8014 (t) cc_final: 0.7543 (p) REVERT: E 60 LEU cc_start: 0.9317 (mt) cc_final: 0.8867 (mt) REVERT: E 94 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 105 GLU cc_start: 0.8806 (tt0) cc_final: 0.8436 (mt-10) REVERT: F 59 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8563 (tttt) REVERT: F 88 TYR cc_start: 0.8747 (m-10) cc_final: 0.8018 (m-10) REVERT: G 90 ASP cc_start: 0.8273 (t0) cc_final: 0.8035 (t0) REVERT: G 91 GLU cc_start: 0.8841 (tt0) cc_final: 0.8484 (tp30) REVERT: G 92 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7567 (mt-10) REVERT: H 30 ARG cc_start: 0.8264 (ptp-170) cc_final: 0.8034 (mtp180) REVERT: H 65 ASP cc_start: 0.9282 (t70) cc_final: 0.9008 (t0) REVERT: H 76 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: H 80 TYR cc_start: 0.8367 (m-10) cc_final: 0.7956 (m-10) REVERT: H 102 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7936 (tm-30) REVERT: K 51 THR cc_start: 0.9179 (p) cc_final: 0.8604 (t) REVERT: K 55 ILE cc_start: 0.7528 (mm) cc_final: 0.6919 (mm) REVERT: K 71 TRP cc_start: 0.6582 (m100) cc_final: 0.6106 (m100) REVERT: K 95 HIS cc_start: 0.9062 (m90) cc_final: 0.8630 (m90) REVERT: K 109 PHE cc_start: 0.8779 (t80) cc_final: 0.7789 (t80) REVERT: K 113 GLN cc_start: 0.7792 (pm20) cc_final: 0.7415 (pm20) REVERT: K 131 GLU cc_start: 0.9189 (mp0) cc_final: 0.8688 (pm20) REVERT: K 147 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7773 (tm-30) REVERT: K 196 ASP cc_start: 0.9280 (m-30) cc_final: 0.8442 (t0) REVERT: K 197 LEU cc_start: 0.8978 (mm) cc_final: 0.8711 (mm) REVERT: K 210 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.8076 (m) REVERT: K 238 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7374 (pt) REVERT: K 257 TYR cc_start: 0.9509 (OUTLIER) cc_final: 0.9275 (t80) REVERT: K 266 MET cc_start: 0.8293 (ttp) cc_final: 0.7953 (ttm) outliers start: 40 outliers final: 30 residues processed: 255 average time/residue: 0.1139 time to fit residues: 41.1670 Evaluate side-chains 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE 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 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 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 120 VAL 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 213 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: 20.0000 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 105 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.104729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064231 restraints weight = 44319.125| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.86 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 14904 Z= 0.218 Angle : 0.726 27.266 21354 Z= 0.397 Chirality : 0.060 2.067 2431 Planarity : 0.006 0.112 1730 Dihedral : 29.714 163.953 4306 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.11 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 19.59 % Favored : 75.35 % 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: 1.05 (0.26), residues: 1028 helix: 2.15 (0.21), residues: 617 sheet: -1.66 (0.85), residues: 36 loop : -1.63 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.026 0.002 TYR C 57 PHE 0.022 0.002 PHE K 124 TRP 0.034 0.004 TRP K 276 HIS 0.023 0.002 HIS K 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (14899) covalent geometry : angle 0.72379 / 0.40 (21348) hydrogen bonds : bond 0.05191 / 3.47 ( 829) hydrogen bonds : angle 3.32088 / 2.40 ( 2098) metal coordination : bond 0.01315 / 0.65 ( 4) metal coordination : angle 3.47849 / 1.94 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 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 280 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9153 (tt0) REVERT: B 93 GLN cc_start: 0.8518 (mp10) cc_final: 0.8301 (mp10) REVERT: C 41 GLU cc_start: 0.7776 (mp0) cc_final: 0.7552 (mp0) REVERT: C 90 ASP cc_start: 0.8329 (t70) cc_final: 0.7986 (t70) REVERT: C 91 GLU cc_start: 0.8257 (pm20) cc_final: 0.7667 (pm20) REVERT: C 92 GLU cc_start: 0.8406 (mp0) cc_final: 0.7530 (mp0) REVERT: D 80 TYR cc_start: 0.8282 (m-10) cc_final: 0.7996 (m-80) REVERT: E 45 THR cc_start: 0.8034 (t) cc_final: 0.7585 (p) REVERT: E 60 LEU cc_start: 0.9235 (mt) cc_final: 0.8966 (mt) REVERT: E 94 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 105 GLU cc_start: 0.8264 (tt0) cc_final: 0.7840 (mt-10) REVERT: F 59 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8329 (tttt) REVERT: G 90 ASP cc_start: 0.8171 (t0) cc_final: 0.7900 (t0) REVERT: G 91 GLU cc_start: 0.8521 (tt0) cc_final: 0.8301 (tp30) REVERT: G 92 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7502 (mt-10) REVERT: H 65 ASP cc_start: 0.8985 (t70) cc_final: 0.8662 (t0) REVERT: H 80 TYR cc_start: 0.8133 (m-10) cc_final: 0.7850 (m-10) REVERT: H 102 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7642 (tm-30) REVERT: K 51 THR cc_start: 0.9109 (p) cc_final: 0.8531 (t) REVERT: K 95 HIS cc_start: 0.9264 (m-70) cc_final: 0.8928 (m90) REVERT: K 109 PHE cc_start: 0.8746 (t80) cc_final: 0.7733 (t80) REVERT: K 131 GLU cc_start: 0.9036 (mp0) cc_final: 0.8514 (pm20) REVERT: K 196 ASP cc_start: 0.9318 (m-30) cc_final: 0.8421 (t0) REVERT: K 197 LEU cc_start: 0.9057 (mm) cc_final: 0.8797 (mm) REVERT: K 259 ASP cc_start: 0.9648 (OUTLIER) cc_final: 0.9281 (m-30) outliers start: 44 outliers final: 32 residues processed: 264 average time/residue: 0.1139 time to fit residues: 42.5839 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 113 SER 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 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 47 VAL 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 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 259 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 147 GLN ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.105896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066264 restraints weight = 45040.077| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.75 r_work: 0.2951 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14904 Z= 0.167 Angle : 0.707 27.226 21354 Z= 0.387 Chirality : 0.060 2.072 2431 Planarity : 0.006 0.114 1730 Dihedral : 29.685 164.254 4306 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.60 % Favored : 96.11 % Rotamer: Outliers : 4.26 % Allowed : 20.97 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1028 helix: 2.26 (0.21), residues: 617 sheet: -0.95 (1.01), residues: 30 loop : -1.65 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.023 0.002 TYR C 57 PHE 0.020 0.002 PHE K 124 TRP 0.039 0.005 TRP K 188 HIS 0.011 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14899) covalent geometry : angle 0.70529 / 0.39 (21348) hydrogen bonds : bond 0.04808 / 3.20 ( 829) hydrogen bonds : angle 3.22490 / 2.33 ( 2098) metal coordination : bond 0.00988 / 0.49 ( 4) metal coordination : angle 3.11694 / 1.74 ( 6) Misc. bond : bond 0.00118 / 0.06 ( 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 273 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9030 (m-10) cc_final: 0.8822 (m-10) REVERT: C 41 GLU cc_start: 0.8379 (mp0) cc_final: 0.8155 (mp0) REVERT: C 90 ASP cc_start: 0.8675 (t70) cc_final: 0.8302 (t0) REVERT: C 91 GLU cc_start: 0.8581 (pm20) cc_final: 0.7963 (pm20) REVERT: C 92 GLU cc_start: 0.8765 (mp0) cc_final: 0.7827 (mp0) REVERT: E 45 THR cc_start: 0.8112 (t) cc_final: 0.7655 (p) REVERT: E 60 LEU cc_start: 0.9263 (mt) cc_final: 0.9007 (mt) REVERT: E 105 GLU cc_start: 0.8772 (tt0) cc_final: 0.8354 (mt-10) REVERT: F 59 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8595 (tttt) REVERT: F 88 TYR cc_start: 0.8713 (m-10) cc_final: 0.8002 (m-10) REVERT: G 90 ASP cc_start: 0.8411 (t0) cc_final: 0.8211 (t0) REVERT: G 91 GLU cc_start: 0.8825 (tt0) cc_final: 0.8518 (tp30) REVERT: G 92 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7570 (mt-10) REVERT: H 30 ARG cc_start: 0.8232 (ptp-170) cc_final: 0.8024 (mtp180) REVERT: H 65 ASP cc_start: 0.9191 (t70) cc_final: 0.8891 (t0) REVERT: H 80 TYR cc_start: 0.8246 (m-10) cc_final: 0.7740 (m-10) REVERT: K 95 HIS cc_start: 0.9112 (m90) cc_final: 0.8851 (m90) REVERT: K 100 GLN cc_start: 0.9011 (tp40) cc_final: 0.8728 (mm-40) REVERT: K 109 PHE cc_start: 0.8754 (t80) cc_final: 0.7765 (t80) REVERT: K 113 GLN cc_start: 0.7745 (pm20) cc_final: 0.7406 (pm20) REVERT: K 147 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: K 196 ASP cc_start: 0.9291 (m-30) cc_final: 0.8477 (t0) REVERT: K 197 LEU cc_start: 0.9008 (mm) cc_final: 0.8733 (mm) REVERT: K 257 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8720 (t80) outliers start: 37 outliers final: 27 residues processed: 257 average time/residue: 0.1148 time to fit residues: 41.8551 Evaluate side-chains 254 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 52 SER 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 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 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 194 ASP 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 236 LEU Chi-restraints excluded: chain K residue 257 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 104 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.106013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066296 restraints weight = 45360.674| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.78 r_work: 0.2957 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3605 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= 0.160 Angle : 0.714 27.247 21354 Z= 0.389 Chirality : 0.059 2.069 2431 Planarity : 0.005 0.115 1730 Dihedral : 29.630 164.648 4306 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.79 % Favored : 95.91 % Rotamer: Outliers : 3.34 % Allowed : 21.77 % Favored : 74.88 % 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: 1.23 (0.27), residues: 1028 helix: 2.30 (0.21), residues: 617 sheet: -1.77 (0.80), residues: 44 loop : -1.55 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.019 0.002 TYR C 57 PHE 0.016 0.001 PHE K 124 TRP 0.036 0.005 TRP K 276 HIS 0.009 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (14899) covalent geometry : angle 0.71215 / 0.39 (21348) hydrogen bonds : bond 0.04755 / 3.14 ( 829) hydrogen bonds : angle 3.22040 / 2.33 ( 2098) metal coordination : bond 0.00792 / 0.40 ( 4) metal coordination : angle 2.85339 / 1.57 ( 6) Misc. bond : bond 0.00120 / 0.06 ( 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: 29 poor density : 234 time to evaluate : 0.328 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: B 30 THR cc_start: 0.9210 (p) cc_final: 0.8933 (t) REVERT: B 88 TYR cc_start: 0.9042 (m-10) cc_final: 0.8825 (m-10) REVERT: B 93 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: C 90 ASP cc_start: 0.8686 (t70) cc_final: 0.8284 (t0) REVERT: C 91 GLU cc_start: 0.8611 (pm20) cc_final: 0.7969 (pm20) REVERT: C 92 GLU cc_start: 0.8772 (mp0) cc_final: 0.7809 (mp0) REVERT: E 45 THR cc_start: 0.8065 (t) cc_final: 0.7833 (p) REVERT: E 105 GLU cc_start: 0.8769 (tt0) cc_final: 0.8345 (mt-10) REVERT: F 59 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8597 (tttt) REVERT: F 88 TYR cc_start: 0.8634 (m-10) cc_final: 0.7992 (m-10) REVERT: G 38 ASN cc_start: 0.8138 (m-40) cc_final: 0.7802 (m-40) REVERT: G 91 GLU cc_start: 0.8777 (tt0) cc_final: 0.8489 (tp30) REVERT: G 104 GLN cc_start: 0.8643 (mp10) cc_final: 0.8287 (mp10) REVERT: H 65 ASP cc_start: 0.9183 (t70) cc_final: 0.8884 (t0) REVERT: H 80 TYR cc_start: 0.8235 (m-10) cc_final: 0.7818 (m-10) REVERT: K 95 HIS cc_start: 0.9243 (m-70) cc_final: 0.9036 (m90) REVERT: K 109 PHE cc_start: 0.8738 (t80) cc_final: 0.7768 (t80) REVERT: K 113 GLN cc_start: 0.7819 (pm20) cc_final: 0.7420 (pm20) REVERT: K 196 ASP cc_start: 0.9278 (m-30) cc_final: 0.8441 (t0) REVERT: K 197 LEU cc_start: 0.8975 (mm) cc_final: 0.8641 (mm) REVERT: K 257 TYR cc_start: 0.9203 (t80) cc_final: 0.8814 (t80) outliers start: 29 outliers final: 25 residues processed: 251 average time/residue: 0.1143 time to fit residues: 40.7984 Evaluate side-chains 251 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 52 SER 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 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 194 ASP 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 236 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 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: 1.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN H 60 ASN K 95 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** K 246 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 = 0.4004 r_free = 0.4004 target = 0.103944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063998 restraints weight = 44893.503| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.81 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3861 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= 0.245 Angle : 0.763 27.362 21354 Z= 0.408 Chirality : 0.060 2.057 2431 Planarity : 0.006 0.117 1730 Dihedral : 29.783 167.111 4306 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.89 % Favored : 95.82 % Rotamer: Outliers : 4.03 % Allowed : 21.89 % Favored : 74.08 % 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: 0.97 (0.26), residues: 1028 helix: 2.07 (0.21), residues: 616 sheet: -1.73 (0.80), residues: 43 loop : -1.62 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.025 0.002 TYR C 57 PHE 0.029 0.002 PHE A 67 TRP 0.035 0.005 TRP K 188 HIS 0.012 0.002 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (14899) covalent geometry : angle 0.76120 / 0.41 (21348) hydrogen bonds : bond 0.05676 / 3.81 ( 829) hydrogen bonds : angle 3.45691 / 2.49 ( 2098) metal coordination : bond 0.01384 / 0.67 ( 4) metal coordination : angle 2.91483 / 1.63 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 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 256 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.9192 (p) cc_final: 0.8896 (t) REVERT: B 88 TYR cc_start: 0.8766 (m-10) cc_final: 0.7547 (m-10) REVERT: C 90 ASP cc_start: 0.8524 (t70) cc_final: 0.7991 (t0) REVERT: C 91 GLU cc_start: 0.8350 (pm20) cc_final: 0.7627 (pm20) REVERT: C 92 GLU cc_start: 0.8414 (mp0) cc_final: 0.7331 (mp0) REVERT: D 80 TYR cc_start: 0.8402 (m-10) cc_final: 0.7624 (m-10) REVERT: E 45 THR cc_start: 0.8070 (t) cc_final: 0.7342 (p) REVERT: E 94 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7825 (mm-30) REVERT: F 59 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8391 (tttt) REVERT: F 88 TYR cc_start: 0.8380 (m-10) cc_final: 0.7592 (m-10) REVERT: H 65 ASP cc_start: 0.8980 (t70) cc_final: 0.8671 (t0) REVERT: H 80 TYR cc_start: 0.8105 (m-10) cc_final: 0.7627 (m-10) REVERT: H 102 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7785 (tm-30) REVERT: K 100 GLN cc_start: 0.9119 (tp40) cc_final: 0.8822 (mm-40) REVERT: K 109 PHE cc_start: 0.8746 (t80) cc_final: 0.7858 (t80) REVERT: K 113 GLN cc_start: 0.7760 (pm20) cc_final: 0.7278 (pm20) REVERT: K 133 HIS cc_start: 0.6495 (m90) cc_final: 0.6068 (m90) REVERT: K 196 ASP cc_start: 0.9320 (m-30) cc_final: 0.8477 (t0) REVERT: K 197 LEU cc_start: 0.9111 (mm) cc_final: 0.8781 (mm) REVERT: K 257 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8812 (t80) outliers start: 35 outliers final: 26 residues processed: 243 average time/residue: 0.1154 time to fit residues: 39.6777 Evaluate side-chains 241 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 52 SER 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 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 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 120 VAL 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 238 ILE Chi-restraints excluded: chain K residue 257 TYR 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: 0.2980 chunk 2 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.105913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065931 restraints weight = 45051.059| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.80 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3921 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= 0.148 Angle : 0.710 27.136 21354 Z= 0.388 Chirality : 0.060 2.081 2431 Planarity : 0.005 0.117 1730 Dihedral : 29.613 165.943 4306 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.40 % Favored : 96.40 % Rotamer: Outliers : 2.30 % Allowed : 23.62 % Favored : 74.08 % 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: 1.26 (0.27), residues: 1028 helix: 2.31 (0.21), residues: 616 sheet: -1.74 (0.81), residues: 44 loop : -1.51 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 76 TYR 0.014 0.002 TYR C 57 PHE 0.026 0.002 PHE A 67 TRP 0.028 0.004 TRP K 276 HIS 0.008 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (14899) covalent geometry : angle 0.70901 / 0.39 (21348) hydrogen bonds : bond 0.04570 / 3.00 ( 829) hydrogen bonds : angle 3.23928 / 2.33 ( 2098) metal coordination : bond 0.00654 / 0.32 ( 4) metal coordination : angle 2.60136 / 1.48 ( 6) Misc. bond : bond 0.00099 / 0.05 ( 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 253 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.241 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: B 30 THR cc_start: 0.9097 (p) cc_final: 0.8793 (t) REVERT: C 90 ASP cc_start: 0.8463 (t70) cc_final: 0.7934 (t0) REVERT: C 91 GLU cc_start: 0.8328 (pm20) cc_final: 0.7587 (pm20) REVERT: C 92 GLU cc_start: 0.8419 (mp0) cc_final: 0.7319 (mp0) REVERT: D 29 THR cc_start: 0.6274 (m) cc_final: 0.5976 (t) REVERT: E 45 THR cc_start: 0.8004 (t) cc_final: 0.7570 (p) REVERT: E 56 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8682 (ptpt) REVERT: F 59 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8362 (tttt) REVERT: F 88 TYR cc_start: 0.8307 (m-10) cc_final: 0.7494 (m-10) REVERT: H 65 ASP cc_start: 0.8886 (t70) cc_final: 0.8570 (t0) REVERT: H 80 TYR cc_start: 0.8041 (m-10) cc_final: 0.7527 (m-10) REVERT: K 95 HIS cc_start: 0.9170 (m90) cc_final: 0.8349 (m90) REVERT: K 109 PHE cc_start: 0.8676 (t80) cc_final: 0.8141 (t80) REVERT: K 111 VAL cc_start: 0.9390 (t) cc_final: 0.9177 (m) REVERT: K 113 GLN cc_start: 0.7620 (pm20) cc_final: 0.6825 (pm20) REVERT: K 133 HIS cc_start: 0.6356 (m90) cc_final: 0.5872 (m90) REVERT: K 257 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8749 (t80) outliers start: 20 outliers final: 16 residues processed: 246 average time/residue: 0.1144 time to fit residues: 39.7867 Evaluate side-chains 239 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain D residue 52 SER 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 E residue 118 THR Chi-restraints excluded: chain F residue 96 THR 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 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: 7.9990 chunk 108 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN F 93 GLN G 104 GLN K 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.104270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064354 restraints weight = 45008.364| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.76 r_work: 0.2869 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4051 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 : 0.733 27.316 21354 Z= 0.395 Chirality : 0.060 2.061 2431 Planarity : 0.006 0.119 1730 Dihedral : 29.670 168.134 4306 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.62 % Rotamer: Outliers : 2.19 % Allowed : 23.96 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 1028 helix: 2.22 (0.21), residues: 616 sheet: -1.83 (0.79), residues: 45 loop : -1.54 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.020 0.002 TYR C 57 PHE 0.014 0.002 PHE K 124 TRP 0.026 0.004 TRP K 276 HIS 0.007 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (14899) covalent geometry : angle 0.73153 / 0.39 (21348) hydrogen bonds : bond 0.05083 / 3.39 ( 829) hydrogen bonds : angle 3.35752 / 2.40 ( 2098) metal coordination : bond 0.01123 / 0.55 ( 4) metal coordination : angle 2.87346 / 1.61 ( 6) Misc. bond : bond 0.00078 / 0.04 ( 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 238 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.368 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 30 THR cc_start: 0.9263 (p) cc_final: 0.9051 (t) REVERT: B 88 TYR cc_start: 0.9048 (m-10) cc_final: 0.7853 (m-10) REVERT: C 90 ASP cc_start: 0.8754 (t70) cc_final: 0.8307 (t0) REVERT: C 91 GLU cc_start: 0.8645 (pm20) cc_final: 0.8012 (pm20) REVERT: C 92 GLU cc_start: 0.8769 (mp0) cc_final: 0.7757 (mp0) REVERT: E 45 THR cc_start: 0.8178 (t) cc_final: 0.7679 (p) REVERT: E 94 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8451 (mm-30) REVERT: F 59 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8635 (tttt) REVERT: F 88 TYR cc_start: 0.8687 (m-10) cc_final: 0.8019 (m-10) REVERT: H 65 ASP cc_start: 0.9252 (t70) cc_final: 0.8961 (t0) REVERT: H 80 TYR cc_start: 0.8292 (m-10) cc_final: 0.7795 (m-10) REVERT: K 95 HIS cc_start: 0.9132 (m90) cc_final: 0.8626 (m90) REVERT: K 109 PHE cc_start: 0.8679 (t80) cc_final: 0.8417 (t80) REVERT: K 113 GLN cc_start: 0.7781 (pm20) cc_final: 0.7352 (pm20) REVERT: K 133 HIS cc_start: 0.6985 (m90) cc_final: 0.6460 (m90) REVERT: K 196 ASP cc_start: 0.9249 (m-30) cc_final: 0.8291 (t0) outliers start: 19 outliers final: 17 residues processed: 233 average time/residue: 0.1184 time to fit residues: 38.6246 Evaluate side-chains 233 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR 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 G residue 104 GLN Chi-restraints excluded: chain H residue 43 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 227 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 85 optimal weight: 40.0000 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 50.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS ** 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 = 0.3991 r_free = 0.3991 target = 0.103285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062995 restraints weight = 45387.412| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.86 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 14904 Z= 0.280 Angle : 0.782 27.395 21354 Z= 0.417 Chirality : 0.061 2.056 2431 Planarity : 0.006 0.120 1730 Dihedral : 29.880 170.076 4306 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 2.65 % Allowed : 23.62 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1028 helix: 1.93 (0.21), residues: 616 sheet: -1.39 (0.80), residues: 43 loop : -1.61 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 76 TYR 0.023 0.002 TYR E 54 PHE 0.012 0.002 PHE C 25 TRP 0.026 0.004 TRP K 276 HIS 0.007 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 (14899) covalent geometry : angle 0.78057 / 0.42 (21348) hydrogen bonds : bond 0.05697 / 3.82 ( 829) hydrogen bonds : angle 3.57224 / 2.55 ( 2098) metal coordination : bond 0.01519 / 0.74 ( 4) metal coordination : angle 2.75403 / 1.53 ( 6) Misc. bond : bond 0.00062 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.83 seconds wall clock time: 56 minutes 36.48 seconds (3396.48 seconds total)