Starting phenix.real_space_refine on Sun May 3 09:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.map" model { file = "/net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nr_75869/05_2026/11nr_75869.cif" } resolution = 2.17 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= 0.009 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12066 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 402 Classifications: {'water': 402} Link IDs: {None: 401} Chain: "B" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 395 Classifications: {'water': 395} Link IDs: {None: 394} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 393 Classifications: {'water': 393} Link IDs: {None: 392} Chain: "D" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 404 Classifications: {'water': 404} Link IDs: {None: 403} Time building chain proxies: 3.58, per 1000 atoms: 0.30 Number of scatterers: 12066 At special positions: 0 Unit cell: (100.695, 80.115, 106.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 3574 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 493.9 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 55.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 4.124A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.845A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.600A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 305 removed outlier: 3.601A pdb=" N LEU A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.941A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.839A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.607A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 305 removed outlier: 3.604A pdb=" N LEU B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 306 through 314 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.925A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.855A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.606A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.587A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 4.152A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.855A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.606A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 305 removed outlier: 3.611A pdb=" N LEU D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 305' Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.808A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32 removed outlier: 5.759A pdb=" N GLY B 28 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 5.762A pdb=" N GLY C 28 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.803A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 580 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2163 1.33 - 1.45: 2265 1.45 - 1.57: 6188 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N GLN B 125 " pdb=" CA GLN B 125 " ideal model delta sigma weight residual 1.452 1.497 -0.045 1.25e-02 6.40e+03 1.30e+01 bond pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.61e+00 bond pdb=" N ASN B 70 " pdb=" CA ASN B 70 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.61e+00 bond pdb=" N LEU B 127 " pdb=" CA LEU B 127 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.49e+00 bond pdb=" N ASP B 128 " pdb=" CA ASP B 128 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.31e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 13442 1.48 - 2.95: 822 2.95 - 4.43: 163 4.43 - 5.90: 27 5.90 - 7.38: 10 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.39 -4.59 1.00e+00 1.00e+00 2.11e+01 angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.34 -4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.32 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.29 -4.49 1.00e+00 1.00e+00 2.02e+01 angle pdb=" CA ASP B 67 " pdb=" CB ASP B 67 " pdb=" CG ASP B 67 " ideal model delta sigma weight residual 112.60 116.91 -4.31 1.00e+00 1.00e+00 1.86e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6032 17.44 - 34.87: 362 34.87 - 52.31: 75 52.31 - 69.75: 25 69.75 - 87.19: 10 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA PHE B 299 " pdb=" C PHE B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PHE D 299 " pdb=" C PHE D 299 " pdb=" N SER D 300 " pdb=" CA SER D 300 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA PHE A 299 " pdb=" C PHE A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1181 0.047 - 0.095: 301 0.095 - 0.142: 119 0.142 - 0.189: 34 0.189 - 0.236: 9 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA HIS D 4 " pdb=" N HIS D 4 " pdb=" C HIS D 4 " pdb=" CB HIS D 4 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU D 305 " pdb=" N LEU D 305 " pdb=" C LEU D 305 " pdb=" CB LEU D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA LEU B 305 " pdb=" N LEU B 305 " pdb=" C LEU B 305 " pdb=" CB LEU B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 128 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C ASP B 128 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP B 128 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 125 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLN B 125 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN B 125 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY B 126 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 144 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C PHE D 144 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE D 144 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA D 145 " -0.011 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3761 2.82 - 3.34: 12491 3.34 - 3.86: 23859 3.86 - 4.38: 28346 4.38 - 4.90: 43678 Nonbonded interactions: 112135 Sorted by model distance: nonbonded pdb=" O ARG B 42 " pdb=" OG SER B 45 " model vdw 2.297 3.040 nonbonded pdb=" O ARG C 42 " pdb=" OG SER C 45 " model vdw 2.297 3.040 nonbonded pdb=" O ARG D 42 " pdb=" OG SER D 45 " model vdw 2.298 3.040 nonbonded pdb=" O LEU D 191 " pdb=" O HOH D 401 " model vdw 2.300 3.040 nonbonded pdb=" O HOH A 564 " pdb=" O HOH A 675 " model vdw 2.301 3.040 ... (remaining 112130 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 : 0.005 0.045 10672 Z= 0.353 Angle : 0.808 7.376 14464 Z= 0.540 Chirality : 0.054 0.236 1644 Planarity : 0.005 0.029 1880 Dihedral : 12.706 87.187 3984 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.81 % Allowed : 0.90 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1364 helix: 1.55 (0.20), residues: 708 sheet: -0.90 (0.41), residues: 136 loop : 0.05 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.014 0.002 TYR C 222 PHE 0.024 0.003 PHE A 144 TRP 0.026 0.004 TRP B 147 HIS 0.007 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00497 (10672) covalent geometry : angle 0.80791 (14464) hydrogen bonds : bond 0.14201 ( 580) hydrogen bonds : angle 6.01860 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.506 Fit side-chains REVERT: A 86 LYS cc_start: 0.8258 (mttt) cc_final: 0.8052 (mttp) REVERT: A 139 LYS cc_start: 0.8492 (ptpt) cc_final: 0.7302 (mmtm) REVERT: A 242 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7562 (mmmt) REVERT: A 278 GLU cc_start: 0.8290 (tt0) cc_final: 0.7826 (tp30) REVERT: A 311 LYS cc_start: 0.7913 (tttm) cc_final: 0.7455 (tttp) REVERT: A 325 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7004 (tp30) REVERT: A 341 LYS cc_start: 0.8591 (mttt) cc_final: 0.8385 (mttp) REVERT: B 14 GLU cc_start: 0.8517 (tt0) cc_final: 0.8295 (tm-30) REVERT: B 139 LYS cc_start: 0.8490 (ptpt) cc_final: 0.7264 (mmtm) REVERT: B 207 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8096 (mmtm) REVERT: B 242 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7532 (mmmt) REVERT: B 278 GLU cc_start: 0.8288 (tt0) cc_final: 0.7781 (tp30) REVERT: B 311 LYS cc_start: 0.7879 (tttm) cc_final: 0.7431 (tttp) REVERT: B 325 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6938 (tp30) REVERT: C 139 LYS cc_start: 0.8531 (ptpt) cc_final: 0.7409 (mmtm) REVERT: C 242 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7563 (mmmt) REVERT: C 278 GLU cc_start: 0.8306 (tt0) cc_final: 0.7811 (tp30) REVERT: C 311 LYS cc_start: 0.7963 (tttm) cc_final: 0.7512 (tttp) REVERT: C 325 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7048 (tp30) REVERT: C 341 LYS cc_start: 0.8606 (mttt) cc_final: 0.8397 (mttp) REVERT: D 42 ARG cc_start: 0.6417 (mtp180) cc_final: 0.5973 (mmp80) REVERT: D 139 LYS cc_start: 0.8513 (ptpt) cc_final: 0.7297 (mmtm) REVERT: D 200 ARG cc_start: 0.8755 (tpt-90) cc_final: 0.8456 (tpt-90) REVERT: D 242 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7516 (mmmt) REVERT: D 278 GLU cc_start: 0.8294 (tt0) cc_final: 0.7781 (tp30) REVERT: D 311 LYS cc_start: 0.7869 (tttm) cc_final: 0.7389 (tttp) REVERT: D 317 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6732 (mtmt) REVERT: D 325 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6968 (tp30) REVERT: D 341 LYS cc_start: 0.8600 (mttt) cc_final: 0.8389 (mttp) outliers start: 9 outliers final: 4 residues processed: 162 average time/residue: 1.0397 time to fit residues: 177.0020 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 50 ASN C 60 GLN C 119 ASN D 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113579 restraints weight = 10356.186| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.20 r_work: 0.3162 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.119 Angle : 0.516 5.031 14464 Z= 0.273 Chirality : 0.041 0.144 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.432 58.127 1480 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.44 % Allowed : 5.04 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.75 (0.23), residues: 1364 helix: 2.45 (0.20), residues: 712 sheet: -0.82 (0.35), residues: 196 loop : 0.09 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.015 0.002 TYR B 213 PHE 0.012 0.002 PHE A 144 TRP 0.015 0.002 TRP B 147 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00258 (10672) covalent geometry : angle 0.51562 (14464) hydrogen bonds : bond 0.05110 ( 580) hydrogen bonds : angle 4.48861 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.408 Fit side-chains REVERT: A 139 LYS cc_start: 0.8418 (ptpt) cc_final: 0.7283 (mmtm) REVERT: A 242 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7512 (mmmt) REVERT: A 278 GLU cc_start: 0.8283 (tt0) cc_final: 0.7800 (tp30) REVERT: A 311 LYS cc_start: 0.8000 (tttm) cc_final: 0.7534 (tttp) REVERT: A 325 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7365 (tp30) REVERT: B 14 GLU cc_start: 0.8416 (tt0) cc_final: 0.8135 (tm-30) REVERT: B 139 LYS cc_start: 0.8380 (ptpt) cc_final: 0.7246 (mmtm) REVERT: B 199 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8166 (mmpt) REVERT: B 207 LYS cc_start: 0.8534 (ttmt) cc_final: 0.7943 (mmtm) REVERT: B 242 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7533 (mmmt) REVERT: B 278 GLU cc_start: 0.8295 (tt0) cc_final: 0.7787 (tp30) REVERT: B 311 LYS cc_start: 0.7983 (tttm) cc_final: 0.7528 (tttp) REVERT: B 317 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6704 (mtpp) REVERT: B 325 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7313 (tp30) REVERT: C 139 LYS cc_start: 0.8390 (ptpt) cc_final: 0.7270 (mmtm) REVERT: C 199 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8153 (mmpt) REVERT: C 242 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7576 (mmmt) REVERT: C 278 GLU cc_start: 0.8282 (tt0) cc_final: 0.7744 (tp30) REVERT: C 311 LYS cc_start: 0.7999 (tttm) cc_final: 0.7533 (tttp) REVERT: C 317 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6766 (mtmt) REVERT: C 325 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7376 (tp30) REVERT: D 42 ARG cc_start: 0.6559 (mtp180) cc_final: 0.5964 (mmp80) REVERT: D 139 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7265 (mmtm) REVERT: D 242 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7524 (mmmt) REVERT: D 278 GLU cc_start: 0.8281 (tt0) cc_final: 0.7756 (tp30) REVERT: D 311 LYS cc_start: 0.7945 (tttm) cc_final: 0.7482 (tttp) REVERT: D 317 LYS cc_start: 0.7096 (mmtt) cc_final: 0.6746 (mtmt) REVERT: D 325 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7373 (tp30) outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 0.9783 time to fit residues: 126.1022 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109063 restraints weight = 10392.938| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.20 r_work: 0.3097 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10672 Z= 0.141 Angle : 0.537 5.254 14464 Z= 0.286 Chirality : 0.042 0.156 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.594 56.229 1480 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 6.21 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.81 (0.23), residues: 1364 helix: 2.60 (0.19), residues: 712 sheet: -1.03 (0.32), residues: 252 loop : 0.26 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.021 0.002 TYR B 213 PHE 0.012 0.002 PHE C 144 TRP 0.018 0.003 TRP B 147 HIS 0.006 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00316 (10672) covalent geometry : angle 0.53721 (14464) hydrogen bonds : bond 0.06014 ( 580) hydrogen bonds : angle 4.53886 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.487 Fit side-chains REVERT: A 52 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 139 LYS cc_start: 0.8502 (ptpt) cc_final: 0.7308 (mmtm) REVERT: A 242 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7529 (mmmt) REVERT: A 278 GLU cc_start: 0.8304 (tt0) cc_final: 0.7839 (tp30) REVERT: A 311 LYS cc_start: 0.8003 (tttm) cc_final: 0.7519 (tttp) REVERT: A 325 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7445 (tp30) REVERT: B 14 GLU cc_start: 0.8430 (tt0) cc_final: 0.8161 (tm-30) REVERT: B 52 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: B 139 LYS cc_start: 0.8487 (ptpt) cc_final: 0.7287 (mmtm) REVERT: B 173 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.9003 (t80) REVERT: B 242 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7528 (mmmt) REVERT: B 278 GLU cc_start: 0.8306 (tt0) cc_final: 0.7804 (tp30) REVERT: B 311 LYS cc_start: 0.8015 (tttm) cc_final: 0.7540 (tttp) REVERT: B 325 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7379 (tp30) REVERT: C 49 GLU cc_start: 0.7071 (pm20) cc_final: 0.6738 (pm20) REVERT: C 52 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: C 67 ASP cc_start: 0.7444 (m-30) cc_final: 0.7121 (m-30) REVERT: C 139 LYS cc_start: 0.8505 (ptpt) cc_final: 0.7337 (mmtm) REVERT: C 173 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.9010 (t80) REVERT: C 242 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7484 (mmmt) REVERT: C 278 GLU cc_start: 0.8290 (tt0) cc_final: 0.7789 (tp30) REVERT: C 311 LYS cc_start: 0.8017 (tttm) cc_final: 0.7541 (tttp) REVERT: C 325 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7375 (tp30) REVERT: D 42 ARG cc_start: 0.6642 (mtp180) cc_final: 0.5942 (mmp80) REVERT: D 52 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: D 67 ASP cc_start: 0.7406 (m-30) cc_final: 0.7085 (m-30) REVERT: D 139 LYS cc_start: 0.8510 (ptpt) cc_final: 0.7315 (mmtm) REVERT: D 199 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8136 (mmpt) REVERT: D 242 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7493 (mmmt) REVERT: D 278 GLU cc_start: 0.8285 (tt0) cc_final: 0.7781 (tp30) REVERT: D 311 LYS cc_start: 0.7980 (tttm) cc_final: 0.7503 (tttp) REVERT: D 317 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6807 (mtmt) REVERT: D 325 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7425 (tp30) outliers start: 24 outliers final: 11 residues processed: 127 average time/residue: 0.8780 time to fit residues: 118.2918 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 43 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN D 95 GLN D 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111783 restraints weight = 10460.286| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.19 r_work: 0.3139 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10672 Z= 0.112 Angle : 0.490 5.037 14464 Z= 0.259 Chirality : 0.040 0.141 1644 Planarity : 0.003 0.026 1880 Dihedral : 5.355 55.696 1480 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.52 % Allowed : 6.65 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.99 (0.23), residues: 1364 helix: 2.78 (0.19), residues: 712 sheet: -1.02 (0.32), residues: 252 loop : 0.31 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.017 0.002 TYR A 213 PHE 0.013 0.001 PHE A 144 TRP 0.010 0.002 TRP B 147 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00246 (10672) covalent geometry : angle 0.48958 (14464) hydrogen bonds : bond 0.04976 ( 580) hydrogen bonds : angle 4.33664 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.491 Fit side-chains REVERT: A 42 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6108 (mmp80) REVERT: A 52 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 67 ASP cc_start: 0.7430 (m-30) cc_final: 0.7189 (m-30) REVERT: A 139 LYS cc_start: 0.8376 (ptpt) cc_final: 0.7250 (mmtm) REVERT: A 242 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7546 (mmmt) REVERT: A 278 GLU cc_start: 0.8300 (tt0) cc_final: 0.7824 (tp30) REVERT: A 311 LYS cc_start: 0.7972 (tttm) cc_final: 0.7481 (tttp) REVERT: A 317 LYS cc_start: 0.7286 (mptp) cc_final: 0.6677 (mtpp) REVERT: A 325 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7343 (tp30) REVERT: A 330 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7240 (mmm160) REVERT: B 14 GLU cc_start: 0.8365 (tt0) cc_final: 0.8098 (tm-30) REVERT: B 42 ARG cc_start: 0.6964 (mtp85) cc_final: 0.6080 (mmp80) REVERT: B 67 ASP cc_start: 0.7396 (m-30) cc_final: 0.7152 (m-30) REVERT: B 139 LYS cc_start: 0.8387 (ptpt) cc_final: 0.7237 (mmtm) REVERT: B 173 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8978 (t80) REVERT: B 199 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8160 (mmpt) REVERT: B 242 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7547 (mmmt) REVERT: B 278 GLU cc_start: 0.8309 (tt0) cc_final: 0.7806 (tp30) REVERT: B 311 LYS cc_start: 0.7975 (tttm) cc_final: 0.7491 (tttp) REVERT: B 317 LYS cc_start: 0.7300 (mptp) cc_final: 0.6676 (mtmt) REVERT: B 325 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7375 (tp30) REVERT: C 49 GLU cc_start: 0.7102 (pm20) cc_final: 0.6765 (pm20) REVERT: C 52 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: C 67 ASP cc_start: 0.7418 (m-30) cc_final: 0.7150 (m-30) REVERT: C 139 LYS cc_start: 0.8397 (ptpt) cc_final: 0.7276 (mmtm) REVERT: C 173 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8987 (t80) REVERT: C 199 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8119 (mmpt) REVERT: C 242 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7550 (mmmt) REVERT: C 278 GLU cc_start: 0.8307 (tt0) cc_final: 0.7796 (tp30) REVERT: C 311 LYS cc_start: 0.7961 (tttm) cc_final: 0.7485 (tttp) REVERT: C 317 LYS cc_start: 0.7313 (mptp) cc_final: 0.6694 (mtmt) REVERT: C 325 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7401 (tp30) REVERT: D 42 ARG cc_start: 0.6688 (mtp180) cc_final: 0.5996 (mmp80) REVERT: D 52 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: D 67 ASP cc_start: 0.7409 (m-30) cc_final: 0.7133 (m-30) REVERT: D 139 LYS cc_start: 0.8359 (ptpt) cc_final: 0.7251 (mmtm) REVERT: D 199 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8118 (mmpt) REVERT: D 242 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7547 (mmmt) REVERT: D 278 GLU cc_start: 0.8292 (tt0) cc_final: 0.7778 (tp30) REVERT: D 311 LYS cc_start: 0.7967 (tttm) cc_final: 0.7491 (tttp) REVERT: D 317 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6714 (mtmt) REVERT: D 325 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7370 (tp30) outliers start: 28 outliers final: 12 residues processed: 126 average time/residue: 0.8676 time to fit residues: 115.9026 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110987 restraints weight = 10484.695| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.20 r_work: 0.3128 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.119 Angle : 0.500 5.138 14464 Z= 0.265 Chirality : 0.040 0.144 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.355 55.465 1480 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.70 % Allowed : 7.46 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.00 (0.23), residues: 1364 helix: 2.81 (0.19), residues: 712 sheet: -1.03 (0.32), residues: 252 loop : 0.26 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.019 0.002 TYR D 213 PHE 0.012 0.001 PHE A 144 TRP 0.012 0.002 TRP B 147 HIS 0.004 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00263 (10672) covalent geometry : angle 0.49963 (14464) hydrogen bonds : bond 0.05152 ( 580) hydrogen bonds : angle 4.32073 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.334 Fit side-chains REVERT: A 52 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 139 LYS cc_start: 0.8420 (ptpt) cc_final: 0.7294 (mmtm) REVERT: A 242 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7524 (mmmt) REVERT: A 278 GLU cc_start: 0.8299 (tt0) cc_final: 0.7823 (tp30) REVERT: A 311 LYS cc_start: 0.7984 (tttm) cc_final: 0.7489 (tttp) REVERT: A 317 LYS cc_start: 0.7265 (mptp) cc_final: 0.6637 (mtmt) REVERT: A 325 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7420 (tp30) REVERT: A 330 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7197 (mmm160) REVERT: B 14 GLU cc_start: 0.8369 (tt0) cc_final: 0.8096 (tm-30) REVERT: B 42 ARG cc_start: 0.6973 (mtp85) cc_final: 0.6148 (mmp80) REVERT: B 52 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: B 139 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7272 (mmtm) REVERT: B 173 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8984 (t80) REVERT: B 199 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8160 (mmpt) REVERT: B 242 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7562 (mmmt) REVERT: B 278 GLU cc_start: 0.8311 (tt0) cc_final: 0.7809 (tp30) REVERT: B 311 LYS cc_start: 0.7981 (tttm) cc_final: 0.7493 (tttp) REVERT: B 317 LYS cc_start: 0.7378 (mptp) cc_final: 0.6703 (mtpp) REVERT: B 325 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7379 (tp30) REVERT: C 49 GLU cc_start: 0.7052 (pm20) cc_final: 0.6713 (pm20) REVERT: C 52 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: C 67 ASP cc_start: 0.7445 (m-30) cc_final: 0.7114 (m-30) REVERT: C 139 LYS cc_start: 0.8410 (ptpt) cc_final: 0.7317 (mmtm) REVERT: C 173 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8991 (t80) REVERT: C 199 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8125 (mmpt) REVERT: C 242 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7508 (mmmt) REVERT: C 278 GLU cc_start: 0.8313 (tt0) cc_final: 0.7797 (tp30) REVERT: C 311 LYS cc_start: 0.7986 (tttm) cc_final: 0.7512 (tttp) REVERT: C 325 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7372 (tp30) REVERT: C 330 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7260 (mmm160) REVERT: D 42 ARG cc_start: 0.6774 (mtp180) cc_final: 0.5966 (mmp80) REVERT: D 52 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: D 67 ASP cc_start: 0.7399 (m-30) cc_final: 0.7063 (m-30) REVERT: D 139 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7288 (mmtm) REVERT: D 242 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7497 (mmmt) REVERT: D 278 GLU cc_start: 0.8292 (tt0) cc_final: 0.7796 (tp30) REVERT: D 311 LYS cc_start: 0.7967 (tttm) cc_final: 0.7480 (tttp) REVERT: D 317 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6666 (mtmt) REVERT: D 325 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7389 (tp30) outliers start: 30 outliers final: 14 residues processed: 130 average time/residue: 0.8575 time to fit residues: 118.2999 Evaluate side-chains 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 2 HIS B 95 GLN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109573 restraints weight = 10526.634| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.20 r_work: 0.3078 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10672 Z= 0.129 Angle : 0.519 5.299 14464 Z= 0.277 Chirality : 0.041 0.150 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.455 55.649 1480 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.79 % Allowed : 7.37 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.94 (0.23), residues: 1364 helix: 2.78 (0.19), residues: 712 sheet: -1.04 (0.32), residues: 252 loop : 0.21 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 257 TYR 0.021 0.002 TYR B 213 PHE 0.013 0.001 PHE A 144 TRP 0.013 0.002 TRP B 147 HIS 0.004 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00288 (10672) covalent geometry : angle 0.51930 (14464) hydrogen bonds : bond 0.05520 ( 580) hydrogen bonds : angle 4.37644 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.453 Fit side-chains REVERT: A 52 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: A 139 LYS cc_start: 0.8470 (ptpt) cc_final: 0.7367 (mmtm) REVERT: A 152 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8690 (pttp) REVERT: A 242 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7589 (mmmt) REVERT: A 278 GLU cc_start: 0.8354 (tt0) cc_final: 0.7895 (tp30) REVERT: A 311 LYS cc_start: 0.8005 (tttm) cc_final: 0.7504 (tttp) REVERT: A 317 LYS cc_start: 0.7375 (mptp) cc_final: 0.6737 (mtpp) REVERT: A 325 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7409 (tp30) REVERT: A 330 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7354 (mmm160) REVERT: B 14 GLU cc_start: 0.8430 (tt0) cc_final: 0.8166 (tm-30) REVERT: B 42 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6166 (mmp80) REVERT: B 52 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: B 139 LYS cc_start: 0.8468 (ptpt) cc_final: 0.7347 (mmtm) REVERT: B 152 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8659 (pttp) REVERT: B 173 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8999 (t80) REVERT: B 199 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8176 (mmpt) REVERT: B 278 GLU cc_start: 0.8340 (tt0) cc_final: 0.7855 (tp30) REVERT: B 311 LYS cc_start: 0.8010 (tttm) cc_final: 0.7517 (tttp) REVERT: B 317 LYS cc_start: 0.7391 (mptp) cc_final: 0.6739 (mtpp) REVERT: B 325 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7399 (tp30) REVERT: C 49 GLU cc_start: 0.7042 (pm20) cc_final: 0.6713 (pm20) REVERT: C 52 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 67 ASP cc_start: 0.7495 (m-30) cc_final: 0.7130 (m-30) REVERT: C 139 LYS cc_start: 0.8464 (ptpt) cc_final: 0.7389 (mmtm) REVERT: C 173 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.9011 (t80) REVERT: C 199 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8150 (mmpt) REVERT: C 242 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7527 (mmmt) REVERT: C 278 GLU cc_start: 0.8342 (tt0) cc_final: 0.7851 (tp30) REVERT: C 311 LYS cc_start: 0.8015 (tttm) cc_final: 0.7538 (tttp) REVERT: C 317 LYS cc_start: 0.7423 (mptp) cc_final: 0.6749 (mtpp) REVERT: C 325 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7390 (tp30) REVERT: C 330 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7416 (mmm160) REVERT: D 42 ARG cc_start: 0.6787 (mtp180) cc_final: 0.5958 (mmp80) REVERT: D 52 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: D 67 ASP cc_start: 0.7429 (m-30) cc_final: 0.7055 (m-30) REVERT: D 139 LYS cc_start: 0.8458 (ptpt) cc_final: 0.7368 (mmtm) REVERT: D 242 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7520 (mmmt) REVERT: D 278 GLU cc_start: 0.8326 (tt0) cc_final: 0.7861 (tp30) REVERT: D 311 LYS cc_start: 0.7990 (tttm) cc_final: 0.7496 (tttp) REVERT: D 317 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6712 (mtmt) REVERT: D 325 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7438 (tp30) outliers start: 31 outliers final: 15 residues processed: 132 average time/residue: 0.8695 time to fit residues: 121.8501 Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 HIS A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110763 restraints weight = 10397.552| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.19 r_work: 0.3128 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10672 Z= 0.117 Angle : 0.498 5.883 14464 Z= 0.264 Chirality : 0.040 0.142 1644 Planarity : 0.003 0.026 1880 Dihedral : 5.327 55.403 1480 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.79 % Allowed : 8.09 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.01 (0.23), residues: 1364 helix: 2.85 (0.19), residues: 712 sheet: -1.02 (0.32), residues: 252 loop : 0.22 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.018 0.002 TYR D 213 PHE 0.013 0.001 PHE A 144 TRP 0.010 0.002 TRP B 147 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00259 (10672) covalent geometry : angle 0.49839 (14464) hydrogen bonds : bond 0.05039 ( 580) hydrogen bonds : angle 4.27794 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.476 Fit side-chains REVERT: A 52 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: A 139 LYS cc_start: 0.8428 (ptpt) cc_final: 0.7319 (mmtm) REVERT: A 242 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7591 (mmmt) REVERT: A 278 GLU cc_start: 0.8307 (tt0) cc_final: 0.7885 (tp30) REVERT: A 311 LYS cc_start: 0.7965 (tttm) cc_final: 0.7454 (tttp) REVERT: A 317 LYS cc_start: 0.7344 (mptp) cc_final: 0.6702 (mtpp) REVERT: A 325 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7403 (tp30) REVERT: A 330 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7286 (mmm160) REVERT: B 14 GLU cc_start: 0.8338 (tt0) cc_final: 0.8078 (tm-30) REVERT: B 42 ARG cc_start: 0.6953 (mtp85) cc_final: 0.6184 (mmp80) REVERT: B 52 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: B 139 LYS cc_start: 0.8422 (ptpt) cc_final: 0.7307 (mmtm) REVERT: B 173 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8977 (t80) REVERT: B 199 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8191 (mmpt) REVERT: B 278 GLU cc_start: 0.8327 (tt0) cc_final: 0.7831 (tp30) REVERT: B 311 LYS cc_start: 0.7958 (tttm) cc_final: 0.7455 (tttp) REVERT: B 325 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7365 (tp30) REVERT: C 42 ARG cc_start: 0.6869 (mtp85) cc_final: 0.6172 (mmp80) REVERT: C 49 GLU cc_start: 0.7045 (pm20) cc_final: 0.6699 (pm20) REVERT: C 52 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: C 67 ASP cc_start: 0.7476 (m-30) cc_final: 0.7150 (m-30) REVERT: C 139 LYS cc_start: 0.8420 (ptpt) cc_final: 0.7345 (mmtm) REVERT: C 173 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8979 (t80) REVERT: C 199 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8175 (mmpt) REVERT: C 242 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7569 (mmmt) REVERT: C 278 GLU cc_start: 0.8292 (tt0) cc_final: 0.7813 (tp30) REVERT: C 311 LYS cc_start: 0.7968 (tttm) cc_final: 0.7483 (tttp) REVERT: C 325 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7283 (tp30) REVERT: C 330 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7338 (mmm160) REVERT: D 42 ARG cc_start: 0.6763 (mtp180) cc_final: 0.5954 (mmp80) REVERT: D 52 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: D 67 ASP cc_start: 0.7451 (m-30) cc_final: 0.7090 (m-30) REVERT: D 139 LYS cc_start: 0.8413 (ptpt) cc_final: 0.7321 (mmtm) REVERT: D 199 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8148 (mmpt) REVERT: D 242 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7563 (mmmt) REVERT: D 278 GLU cc_start: 0.8291 (tt0) cc_final: 0.7826 (tp30) REVERT: D 311 LYS cc_start: 0.7947 (tttm) cc_final: 0.7442 (tttp) REVERT: D 317 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6673 (mtmt) REVERT: D 325 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7389 (tp30) outliers start: 31 outliers final: 15 residues processed: 131 average time/residue: 0.8569 time to fit residues: 119.2742 Evaluate side-chains 130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109566 restraints weight = 10416.058| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.19 r_work: 0.3112 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10672 Z= 0.126 Angle : 0.516 6.334 14464 Z= 0.274 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.407 55.471 1480 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.79 % Allowed : 8.27 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.95 (0.23), residues: 1364 helix: 2.80 (0.19), residues: 712 sheet: -1.03 (0.32), residues: 252 loop : 0.18 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.020 0.002 TYR B 213 PHE 0.012 0.001 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (10672) covalent geometry : angle 0.51600 (14464) hydrogen bonds : bond 0.05390 ( 580) hydrogen bonds : angle 4.32958 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.483 Fit side-chains REVERT: A 52 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 139 LYS cc_start: 0.8465 (ptpt) cc_final: 0.7338 (mmtm) REVERT: A 152 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8681 (pttp) REVERT: A 242 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7620 (mmmt) REVERT: A 278 GLU cc_start: 0.8299 (tt0) cc_final: 0.7863 (tp30) REVERT: A 311 LYS cc_start: 0.7989 (tttm) cc_final: 0.7481 (tttp) REVERT: A 325 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7332 (tp30) REVERT: A 330 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7333 (mmm160) REVERT: B 14 GLU cc_start: 0.8363 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 42 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6185 (mmp80) REVERT: B 52 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: B 139 LYS cc_start: 0.8463 (ptpt) cc_final: 0.7328 (mmtm) REVERT: B 152 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8641 (pttp) REVERT: B 173 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8996 (t80) REVERT: B 199 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8188 (mmpt) REVERT: B 278 GLU cc_start: 0.8322 (tt0) cc_final: 0.7834 (tp30) REVERT: B 311 LYS cc_start: 0.7997 (tttm) cc_final: 0.7491 (tttp) REVERT: B 325 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7355 (tp30) REVERT: C 42 ARG cc_start: 0.6817 (mtp85) cc_final: 0.6169 (mmp80) REVERT: C 49 GLU cc_start: 0.7039 (pm20) cc_final: 0.6696 (pm20) REVERT: C 52 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: C 67 ASP cc_start: 0.7480 (m-30) cc_final: 0.7156 (m-30) REVERT: C 139 LYS cc_start: 0.8456 (ptpt) cc_final: 0.7362 (mmtm) REVERT: C 152 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8674 (pttp) REVERT: C 173 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8998 (t80) REVERT: C 199 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8183 (mmpt) REVERT: C 242 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7550 (mmmt) REVERT: C 278 GLU cc_start: 0.8295 (tt0) cc_final: 0.7820 (tp30) REVERT: C 311 LYS cc_start: 0.7993 (tttm) cc_final: 0.7504 (tttp) REVERT: C 325 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7380 (tp30) REVERT: C 330 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7397 (mmm160) REVERT: D 42 ARG cc_start: 0.6666 (mtp180) cc_final: 0.5914 (mmp80) REVERT: D 52 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: D 67 ASP cc_start: 0.7387 (m-30) cc_final: 0.7024 (m-30) REVERT: D 139 LYS cc_start: 0.8440 (ptpt) cc_final: 0.7331 (mmtm) REVERT: D 199 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8130 (mmpt) REVERT: D 242 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7561 (mmmt) REVERT: D 278 GLU cc_start: 0.8301 (tt0) cc_final: 0.7837 (tp30) REVERT: D 311 LYS cc_start: 0.7979 (tttm) cc_final: 0.7475 (tttp) REVERT: D 317 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6724 (mtmt) REVERT: D 325 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7428 (tp30) outliers start: 31 outliers final: 15 residues processed: 132 average time/residue: 0.8688 time to fit residues: 121.8753 Evaluate side-chains 134 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111940 restraints weight = 10380.908| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.19 r_work: 0.3145 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10672 Z= 0.109 Angle : 0.488 6.698 14464 Z= 0.258 Chirality : 0.039 0.138 1644 Planarity : 0.003 0.026 1880 Dihedral : 5.219 55.230 1480 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 8.45 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.07 (0.23), residues: 1364 helix: 2.91 (0.19), residues: 712 sheet: -1.01 (0.32), residues: 252 loop : 0.22 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 59 TYR 0.017 0.001 TYR B 213 PHE 0.013 0.001 PHE A 144 TRP 0.009 0.001 TRP B 147 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00242 (10672) covalent geometry : angle 0.48825 (14464) hydrogen bonds : bond 0.04692 ( 580) hydrogen bonds : angle 4.19031 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.344 Fit side-chains REVERT: A 52 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: A 139 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7322 (mmtm) REVERT: A 242 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7606 (mmmt) REVERT: A 278 GLU cc_start: 0.8310 (tt0) cc_final: 0.7881 (tp30) REVERT: A 311 LYS cc_start: 0.7970 (tttm) cc_final: 0.7458 (tttp) REVERT: A 317 LYS cc_start: 0.7324 (mptp) cc_final: 0.6659 (mtpp) REVERT: A 325 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7377 (tp30) REVERT: A 330 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7230 (mmm160) REVERT: B 14 GLU cc_start: 0.8301 (tt0) cc_final: 0.8052 (tm-30) REVERT: B 52 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: B 139 LYS cc_start: 0.8386 (ptpt) cc_final: 0.7310 (mmtm) REVERT: B 152 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8643 (pttp) REVERT: B 173 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8966 (t80) REVERT: B 199 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8200 (mmpt) REVERT: B 278 GLU cc_start: 0.8329 (tt0) cc_final: 0.7835 (tp30) REVERT: B 311 LYS cc_start: 0.7949 (tttm) cc_final: 0.7437 (tttp) REVERT: B 325 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7386 (tp30) REVERT: C 42 ARG cc_start: 0.6809 (mtp85) cc_final: 0.6205 (mmp80) REVERT: C 49 GLU cc_start: 0.7051 (pm20) cc_final: 0.6709 (pm20) REVERT: C 52 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: C 67 ASP cc_start: 0.7473 (m-30) cc_final: 0.7085 (m-30) REVERT: C 95 GLN cc_start: 0.8348 (tt0) cc_final: 0.7281 (tp-100) REVERT: C 139 LYS cc_start: 0.8385 (ptpt) cc_final: 0.7345 (mmtm) REVERT: C 173 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8960 (t80) REVERT: C 199 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8198 (mmpt) REVERT: C 242 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7605 (mmmt) REVERT: C 278 GLU cc_start: 0.8294 (tt0) cc_final: 0.7813 (tp30) REVERT: C 311 LYS cc_start: 0.7954 (tttm) cc_final: 0.7463 (tttp) REVERT: C 325 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7389 (tp30) REVERT: C 330 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7239 (mmm160) REVERT: D 42 ARG cc_start: 0.6628 (mtp180) cc_final: 0.5922 (mmp80) REVERT: D 52 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: D 67 ASP cc_start: 0.7414 (m-30) cc_final: 0.7080 (m-30) REVERT: D 139 LYS cc_start: 0.8371 (ptpt) cc_final: 0.7317 (mmtm) REVERT: D 199 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8155 (mmpt) REVERT: D 242 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7592 (mmmt) REVERT: D 278 GLU cc_start: 0.8303 (tt0) cc_final: 0.7834 (tp30) REVERT: D 311 LYS cc_start: 0.7937 (tttm) cc_final: 0.7430 (tttp) REVERT: D 317 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6680 (mtmt) outliers start: 28 outliers final: 15 residues processed: 132 average time/residue: 0.8248 time to fit residues: 115.5808 Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.0270 chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109921 restraints weight = 10427.767| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.19 r_work: 0.3117 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.125 Angle : 0.519 7.015 14464 Z= 0.275 Chirality : 0.041 0.148 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.356 55.509 1480 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.70 % Allowed : 8.36 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.97 (0.23), residues: 1364 helix: 2.82 (0.19), residues: 712 sheet: -1.03 (0.32), residues: 252 loop : 0.19 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.020 0.002 TYR B 213 PHE 0.013 0.001 PHE A 144 TRP 0.012 0.002 TRP B 147 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00281 (10672) covalent geometry : angle 0.51865 (14464) hydrogen bonds : bond 0.05279 ( 580) hydrogen bonds : angle 4.28593 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.493 Fit side-chains REVERT: A 52 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: A 139 LYS cc_start: 0.8435 (ptpt) cc_final: 0.7340 (mmtm) REVERT: A 242 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7612 (mmmt) REVERT: A 278 GLU cc_start: 0.8302 (tt0) cc_final: 0.7885 (tp30) REVERT: A 311 LYS cc_start: 0.8002 (tttm) cc_final: 0.7486 (tttp) REVERT: A 317 LYS cc_start: 0.7338 (mptp) cc_final: 0.6668 (mtpp) REVERT: A 325 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7327 (tp30) REVERT: A 330 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7332 (mmm160) REVERT: B 14 GLU cc_start: 0.8347 (tt0) cc_final: 0.8087 (tm-30) REVERT: B 52 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: B 139 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7338 (mmtm) REVERT: B 152 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8658 (pttp) REVERT: B 173 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8996 (t80) REVERT: B 199 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8187 (mmpt) REVERT: B 278 GLU cc_start: 0.8328 (tt0) cc_final: 0.7834 (tp30) REVERT: B 325 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7397 (tp30) REVERT: C 42 ARG cc_start: 0.6829 (mtp85) cc_final: 0.6223 (mmp80) REVERT: C 49 GLU cc_start: 0.7052 (pm20) cc_final: 0.6705 (pm20) REVERT: C 52 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: C 67 ASP cc_start: 0.7427 (m-30) cc_final: 0.7101 (m-30) REVERT: C 139 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7361 (mmtm) REVERT: C 152 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8675 (pttp) REVERT: C 173 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8999 (t80) REVERT: C 199 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8179 (mmpt) REVERT: C 242 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7575 (mmmt) REVERT: C 278 GLU cc_start: 0.8298 (tt0) cc_final: 0.7823 (tp30) REVERT: C 311 LYS cc_start: 0.7990 (tttm) cc_final: 0.7499 (tttp) REVERT: C 325 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7311 (tp30) REVERT: C 330 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7387 (mmm160) REVERT: D 42 ARG cc_start: 0.6645 (mtp180) cc_final: 0.5900 (mmp80) REVERT: D 52 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: D 139 LYS cc_start: 0.8414 (ptpt) cc_final: 0.7341 (mmtm) REVERT: D 152 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8653 (pttp) REVERT: D 199 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8158 (mmpt) REVERT: D 242 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7556 (mmmt) REVERT: D 278 GLU cc_start: 0.8302 (tt0) cc_final: 0.7838 (tp30) REVERT: D 317 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6707 (mtmt) outliers start: 30 outliers final: 15 residues processed: 134 average time/residue: 0.8323 time to fit residues: 118.7065 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 330 ARG Chi-restraints excluded: chain D residue 343 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111210 restraints weight = 10412.927| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.20 r_work: 0.3135 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.114 Angle : 0.499 7.019 14464 Z= 0.264 Chirality : 0.040 0.142 1644 Planarity : 0.003 0.026 1880 Dihedral : 5.253 55.404 1480 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.70 % Allowed : 8.63 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.03 (0.23), residues: 1364 helix: 2.87 (0.19), residues: 712 sheet: -1.02 (0.32), residues: 252 loop : 0.21 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 59 TYR 0.018 0.001 TYR B 213 PHE 0.013 0.001 PHE A 144 TRP 0.009 0.001 TRP B 147 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00254 (10672) covalent geometry : angle 0.49931 (14464) hydrogen bonds : bond 0.04868 ( 580) hydrogen bonds : angle 4.19915 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4809.93 seconds wall clock time: 82 minutes 49.57 seconds (4969.57 seconds total)