Starting phenix.real_space_refine on Sun May 3 09:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.map" model { file = "/net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nm_75865/05_2026/11nm_75865.cif" } resolution = 2.19 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 3361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 11853 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: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 345 Classifications: {'water': 345} Link IDs: {None: 344} Chain: "B" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 354 Classifications: {'water': 354} Link IDs: {None: 353} Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 339 Classifications: {'water': 339} Link IDs: {None: 338} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 343 Classifications: {'water': 343} Link IDs: {None: 342} Time building chain proxies: 2.80, per 1000 atoms: 0.24 Number of scatterers: 11853 At special positions: 0 Unit cell: (102.165, 83.055, 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 3361 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: 0.71 Conformation dependent library (CDL) restraints added in 412.1 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: 61 helices and 8 sheets defined 55.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.859A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.964A 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 81 through 85 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: 3.635A 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 314 removed outlier: 3.649A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) 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: 3.822A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.865A 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: 3.638A 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 314 removed outlier: 3.531A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) 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: 3.826A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.867A 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 removed outlier: 3.578A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) 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: 3.638A 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 305 removed outlier: 3.646A pdb=" N LEU C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 306 through 314 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: 3.804A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.638A 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 314 removed outlier: 3.510A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) 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: 6.837A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.323A 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: 6.836A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.320A 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: 6.859A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.318A 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: 6.833A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.320A 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 114 587 hydrogen bonds defined for protein. 1695 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: 1.66 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2070 1.33 - 1.45: 2344 1.45 - 1.57: 6202 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N ILE D 46 " pdb=" CA ILE D 46 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.07e-02 8.73e+03 1.52e+01 bond pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.16e-02 7.43e+03 9.26e+00 bond pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.04e+00 bond pdb=" N TRP D 295 " pdb=" CA TRP D 295 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.22e-02 6.72e+03 8.66e+00 bond pdb=" C PRO C 261 " pdb=" N PRO C 262 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.28e-02 6.10e+03 8.07e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 13601 1.47 - 2.93: 684 2.93 - 4.40: 134 4.40 - 5.86: 32 5.86 - 7.33: 13 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.73 -4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" N GLN C 60 " pdb=" CA GLN C 60 " pdb=" C GLN C 60 " ideal model delta sigma weight residual 111.14 105.89 5.25 1.08e+00 8.57e-01 2.37e+01 angle pdb=" N ALA D 6 " pdb=" CA ALA D 6 " pdb=" C ALA D 6 " ideal model delta sigma weight residual 112.90 106.55 6.35 1.31e+00 5.83e-01 2.35e+01 angle pdb=" N GLN D 60 " pdb=" CA GLN D 60 " pdb=" C GLN D 60 " ideal model delta sigma weight residual 111.07 105.98 5.09 1.07e+00 8.73e-01 2.26e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 6064 17.16 - 34.32: 336 34.32 - 51.49: 73 51.49 - 68.65: 19 68.65 - 85.81: 12 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 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+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 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE C 299 " pdb=" C PHE C 299 " pdb=" N SER C 300 " pdb=" CA SER C 300 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1345 0.062 - 0.123: 253 0.123 - 0.185: 36 0.185 - 0.246: 9 0.246 - 0.308: 1 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LYS C 329 " pdb=" N LYS C 329 " pdb=" C LYS C 329 " pdb=" CB LYS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LEU C 305 " pdb=" N LEU C 305 " pdb=" C LEU C 305 " pdb=" CB LEU C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LEU C 227 " pdb=" N LEU C 227 " pdb=" C LEU C 227 " pdb=" CB LEU C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 292 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU A 292 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 292 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 293 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 292 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C LEU C 292 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU C 292 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 293 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 330 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ARG C 330 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG C 330 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA C 331 " -0.012 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3793 2.82 - 3.34: 12135 3.34 - 3.86: 23160 3.86 - 4.38: 27838 4.38 - 4.90: 42906 Nonbonded interactions: 109832 Sorted by model distance: nonbonded pdb=" OG SER A 38 " pdb=" O HOH A 401 " model vdw 2.304 3.040 nonbonded pdb=" O HOH B 555 " pdb=" O HOH B 616 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR B 240 " pdb=" O HOH B 401 " model vdw 2.305 3.040 nonbonded pdb=" O HOH A 550 " pdb=" O HOH A 622 " model vdw 2.307 3.040 nonbonded pdb=" O HOH D 428 " pdb=" O HOH D 716 " model vdw 2.307 3.040 ... (remaining 109827 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: 3.410 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.450 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 0.042 10672 Z= 0.314 Angle : 0.770 7.327 14464 Z= 0.498 Chirality : 0.051 0.308 1644 Planarity : 0.005 0.034 1880 Dihedral : 12.310 85.811 3984 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.90 % Allowed : 1.53 % Favored : 97.57 % 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: 0.67 (0.23), residues: 1364 helix: 1.28 (0.19), residues: 712 sheet: -1.70 (0.34), residues: 204 loop : 0.40 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 200 TYR 0.018 0.002 TYR A 301 PHE 0.024 0.002 PHE B 144 TRP 0.024 0.004 TRP C 313 HIS 0.005 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00461 (10672) covalent geometry : angle 0.77016 (14464) hydrogen bonds : bond 0.14973 ( 587) hydrogen bonds : angle 6.24199 ( 1695) *********************** 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 194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.375 Fit side-chains REVERT: A 42 ARG cc_start: 0.6611 (mtp180) cc_final: 0.6363 (mmp80) REVERT: A 199 LYS cc_start: 0.8252 (mttt) cc_final: 0.7839 (mmtm) REVERT: A 303 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7035 (tmm160) REVERT: A 311 LYS cc_start: 0.7867 (ttmm) cc_final: 0.7264 (tmmt) REVERT: B 42 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6444 (mmp80) REVERT: B 199 LYS cc_start: 0.8217 (mttt) cc_final: 0.7855 (mmtm) REVERT: B 311 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7240 (tmmt) REVERT: C 42 ARG cc_start: 0.6249 (mtp180) cc_final: 0.5959 (mmp80) REVERT: C 199 LYS cc_start: 0.8463 (mttt) cc_final: 0.7875 (mmtm) REVERT: C 303 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7001 (mtm-85) REVERT: C 311 LYS cc_start: 0.7762 (tptt) cc_final: 0.7256 (tmmt) REVERT: D 42 ARG cc_start: 0.6699 (mtp180) cc_final: 0.6290 (mmp80) REVERT: D 199 LYS cc_start: 0.8539 (mttt) cc_final: 0.7969 (mmtm) REVERT: D 242 LYS cc_start: 0.8129 (mttm) cc_final: 0.7627 (mmmm) REVERT: D 303 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7088 (tmm160) REVERT: D 311 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7235 (tmmt) outliers start: 10 outliers final: 6 residues processed: 192 average time/residue: 0.8334 time to fit residues: 168.8815 Evaluate side-chains 88 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 2 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS 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: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 180 ASN A 241 GLN B 85 GLN B 241 GLN C 85 GLN C 136 GLN C 241 GLN D 180 ASN D 241 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104622 restraints weight = 10444.339| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.35 r_work: 0.3010 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10672 Z= 0.115 Angle : 0.508 6.448 14464 Z= 0.270 Chirality : 0.041 0.151 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.412 56.045 1484 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 7.55 % Favored : 91.01 % 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: 1.60 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 712 sheet: -1.10 (0.32), residues: 252 loop : 0.51 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 303 TYR 0.014 0.002 TYR C 213 PHE 0.012 0.001 PHE B 144 TRP 0.011 0.002 TRP A 147 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00229 (10672) covalent geometry : angle 0.50768 (14464) hydrogen bonds : bond 0.04871 ( 587) hydrogen bonds : angle 4.71256 ( 1695) *********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.448 Fit side-chains REVERT: A 42 ARG cc_start: 0.6621 (mtp180) cc_final: 0.6292 (mmp80) REVERT: A 199 LYS cc_start: 0.8467 (mttt) cc_final: 0.7831 (mmtm) REVERT: A 303 ARG cc_start: 0.7806 (mtm180) cc_final: 0.6996 (tmm160) REVERT: A 311 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7272 (tmmt) REVERT: B 42 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6355 (mmp80) REVERT: B 199 LYS cc_start: 0.8471 (mttt) cc_final: 0.7801 (mmtm) REVERT: B 311 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7208 (tmmt) REVERT: C 42 ARG cc_start: 0.6485 (mtp180) cc_final: 0.6175 (mmp80) REVERT: C 199 LYS cc_start: 0.8526 (mttt) cc_final: 0.7849 (mmtm) REVERT: C 303 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7088 (mtm-85) REVERT: C 311 LYS cc_start: 0.7813 (tptt) cc_final: 0.7281 (tmmt) REVERT: D 42 ARG cc_start: 0.6684 (mtp180) cc_final: 0.6233 (mmp80) REVERT: D 199 LYS cc_start: 0.8477 (mttt) cc_final: 0.7808 (mmtm) REVERT: D 242 LYS cc_start: 0.8047 (mttm) cc_final: 0.7555 (mmmm) REVERT: D 303 ARG cc_start: 0.7795 (mtm180) cc_final: 0.6965 (tmm160) REVERT: D 311 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7191 (tmmt) outliers start: 16 outliers final: 7 residues processed: 107 average time/residue: 0.9680 time to fit residues: 109.1044 Evaluate side-chains 82 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS 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 17 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 HIS A 219 HIS A 241 GLN B 241 GLN C 241 GLN D 219 HIS D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103428 restraints weight = 10503.737| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.37 r_work: 0.3017 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10672 Z= 0.109 Angle : 0.490 5.595 14464 Z= 0.258 Chirality : 0.041 0.144 1644 Planarity : 0.004 0.028 1880 Dihedral : 5.339 57.222 1484 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.07 % Allowed : 7.55 % Favored : 90.38 % 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: 1.88 (0.23), residues: 1364 helix: 2.62 (0.19), residues: 712 sheet: -1.05 (0.32), residues: 252 loop : 0.40 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 200 TYR 0.016 0.002 TYR B 213 PHE 0.012 0.001 PHE A 144 TRP 0.012 0.002 TRP B 147 HIS 0.002 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00223 (10672) covalent geometry : angle 0.49043 (14464) hydrogen bonds : bond 0.04897 ( 587) hydrogen bonds : angle 4.50362 ( 1695) *********************** 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 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.416 Fit side-chains REVERT: A 42 ARG cc_start: 0.6690 (mtp180) cc_final: 0.6370 (mmp80) REVERT: A 52 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: A 67 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.5782 (t0) REVERT: A 199 LYS cc_start: 0.8485 (mttt) cc_final: 0.7856 (mmtm) REVERT: A 303 ARG cc_start: 0.7772 (mtm180) cc_final: 0.6974 (tmm160) REVERT: A 311 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7194 (tmmt) REVERT: A 321 LYS cc_start: 0.7377 (mppt) cc_final: 0.7024 (ttpt) REVERT: B 42 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6378 (mmp80) REVERT: B 52 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: B 199 LYS cc_start: 0.8484 (mttt) cc_final: 0.7837 (mmtm) REVERT: B 303 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7028 (tmm160) REVERT: B 311 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7231 (tmmt) REVERT: C 42 ARG cc_start: 0.6509 (mtp180) cc_final: 0.6080 (mmp80) REVERT: C 52 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: C 199 LYS cc_start: 0.8528 (mttt) cc_final: 0.7873 (mmtm) REVERT: C 303 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7008 (mtm-85) REVERT: C 311 LYS cc_start: 0.7817 (tptt) cc_final: 0.7268 (tmmt) REVERT: D 42 ARG cc_start: 0.6701 (mtp180) cc_final: 0.6244 (mmp80) REVERT: D 199 LYS cc_start: 0.8500 (mttt) cc_final: 0.7849 (mmtm) REVERT: D 242 LYS cc_start: 0.8102 (mttm) cc_final: 0.7606 (mmmm) REVERT: D 303 ARG cc_start: 0.7777 (mtm180) cc_final: 0.6957 (tmm160) REVERT: D 311 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7179 (tmmt) REVERT: D 321 LYS cc_start: 0.7348 (mppt) cc_final: 0.7005 (ttpt) outliers start: 23 outliers final: 7 residues processed: 101 average time/residue: 0.9006 time to fit residues: 96.0396 Evaluate side-chains 85 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099381 restraints weight = 10580.474| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.35 r_work: 0.2936 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10672 Z= 0.162 Angle : 0.570 5.940 14464 Z= 0.301 Chirality : 0.044 0.154 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.586 55.627 1484 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.98 % Allowed : 8.27 % Favored : 89.75 % 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: 1.64 (0.23), residues: 1364 helix: 2.48 (0.19), residues: 712 sheet: -1.16 (0.32), residues: 252 loop : 0.16 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 59 TYR 0.025 0.002 TYR A 213 PHE 0.014 0.002 PHE C 144 TRP 0.015 0.003 TRP A 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00358 (10672) covalent geometry : angle 0.56952 (14464) hydrogen bonds : bond 0.06305 ( 587) hydrogen bonds : angle 4.69564 ( 1695) *********************** 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 99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.486 Fit side-chains REVERT: A 42 ARG cc_start: 0.6676 (mtp180) cc_final: 0.6387 (mmp80) REVERT: A 52 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: A 199 LYS cc_start: 0.8550 (mttt) cc_final: 0.7932 (mmtm) REVERT: A 311 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7355 (tmmt) REVERT: B 42 ARG cc_start: 0.6689 (mtp180) cc_final: 0.6372 (mmp80) REVERT: B 52 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: B 199 LYS cc_start: 0.8539 (mttt) cc_final: 0.7914 (mmtm) REVERT: B 311 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7425 (tmmt) REVERT: C 42 ARG cc_start: 0.6455 (mtp180) cc_final: 0.6156 (mmp80) REVERT: C 52 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: C 67 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6063 (t0) REVERT: C 199 LYS cc_start: 0.8578 (mttt) cc_final: 0.7914 (mmtm) REVERT: C 303 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7054 (mtm-85) REVERT: C 311 LYS cc_start: 0.7896 (tptt) cc_final: 0.7296 (tmmt) REVERT: C 321 LYS cc_start: 0.7462 (mppt) cc_final: 0.7000 (ttpt) REVERT: D 42 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6362 (mmp80) REVERT: D 67 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6094 (t0) REVERT: D 139 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8038 (ptpp) REVERT: D 199 LYS cc_start: 0.8553 (mttt) cc_final: 0.7900 (mmtm) REVERT: D 242 LYS cc_start: 0.8124 (mttm) cc_final: 0.7623 (mmmm) REVERT: D 311 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7380 (tmmt) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 0.8505 time to fit residues: 85.4348 Evaluate side-chains 88 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100275 restraints weight = 10514.942| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.36 r_work: 0.2978 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10672 Z= 0.124 Angle : 0.514 5.758 14464 Z= 0.271 Chirality : 0.042 0.146 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.425 55.278 1484 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.07 % Allowed : 8.00 % Favored : 89.93 % 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: 1.78 (0.23), residues: 1364 helix: 2.65 (0.19), residues: 712 sheet: -1.18 (0.31), residues: 252 loop : 0.18 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 59 TYR 0.020 0.002 TYR A 213 PHE 0.015 0.001 PHE C 144 TRP 0.011 0.002 TRP A 147 HIS 0.003 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00265 (10672) covalent geometry : angle 0.51355 (14464) hydrogen bonds : bond 0.05369 ( 587) hydrogen bonds : angle 4.56122 ( 1695) *********************** 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 100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.455 Fit side-chains REVERT: A 42 ARG cc_start: 0.6658 (mtp180) cc_final: 0.6410 (mmp80) REVERT: A 52 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: A 139 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7990 (ptpp) REVERT: A 199 LYS cc_start: 0.8540 (mttt) cc_final: 0.7911 (mmtm) REVERT: A 311 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7296 (tmmt) REVERT: A 321 LYS cc_start: 0.7387 (mppt) cc_final: 0.7062 (mptp) REVERT: B 42 ARG cc_start: 0.6824 (mtp180) cc_final: 0.6359 (mmp80) REVERT: B 52 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: B 199 LYS cc_start: 0.8528 (mttt) cc_final: 0.7892 (mmtm) REVERT: B 311 LYS cc_start: 0.7967 (ttmm) cc_final: 0.7366 (tmmt) REVERT: C 42 ARG cc_start: 0.6491 (mtp180) cc_final: 0.6192 (mmp80) REVERT: C 52 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6957 (tp30) REVERT: C 199 LYS cc_start: 0.8558 (mttt) cc_final: 0.7902 (mmtm) REVERT: C 303 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7207 (tmm160) REVERT: C 311 LYS cc_start: 0.7845 (tptt) cc_final: 0.7274 (tmmt) REVERT: C 321 LYS cc_start: 0.7379 (mppt) cc_final: 0.7063 (mptp) REVERT: D 42 ARG cc_start: 0.6753 (mtp180) cc_final: 0.6319 (mmp80) REVERT: D 67 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.5936 (t0) REVERT: D 139 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7981 (ptpp) REVERT: D 199 LYS cc_start: 0.8529 (mttt) cc_final: 0.7875 (mmtm) REVERT: D 242 LYS cc_start: 0.8138 (mttm) cc_final: 0.7633 (mmmm) REVERT: D 311 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7269 (tmmt) REVERT: D 321 LYS cc_start: 0.7363 (mppt) cc_final: 0.7041 (mptp) outliers start: 23 outliers final: 10 residues processed: 97 average time/residue: 0.8678 time to fit residues: 88.9868 Evaluate side-chains 89 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102851 restraints weight = 10557.612| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.37 r_work: 0.2993 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10672 Z= 0.105 Angle : 0.479 6.007 14464 Z= 0.250 Chirality : 0.040 0.140 1644 Planarity : 0.003 0.028 1880 Dihedral : 5.242 55.268 1484 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.71 % Allowed : 8.81 % Favored : 89.48 % 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: 1.98 (0.23), residues: 1364 helix: 2.83 (0.19), residues: 712 sheet: -1.06 (0.32), residues: 252 loop : 0.23 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.017 0.001 TYR C 213 PHE 0.013 0.001 PHE C 144 TRP 0.008 0.001 TRP C 147 HIS 0.002 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00217 (10672) covalent geometry : angle 0.47871 (14464) hydrogen bonds : bond 0.04644 ( 587) hydrogen bonds : angle 4.39581 ( 1695) *********************** 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 98 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.318 Fit side-chains REVERT: A 42 ARG cc_start: 0.6663 (mtp180) cc_final: 0.6338 (mmp80) REVERT: A 52 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: A 139 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8009 (ptpp) REVERT: A 199 LYS cc_start: 0.8519 (mttt) cc_final: 0.7883 (mmtm) REVERT: A 311 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7278 (tmmt) REVERT: A 321 LYS cc_start: 0.7405 (mppt) cc_final: 0.7092 (mptp) REVERT: B 42 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6392 (mmp80) REVERT: B 52 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: B 199 LYS cc_start: 0.8510 (mttt) cc_final: 0.7863 (mmtm) REVERT: B 311 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7355 (tmmt) REVERT: B 321 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7228 (mppt) REVERT: C 42 ARG cc_start: 0.6504 (mtp180) cc_final: 0.6075 (mmp80) REVERT: C 52 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: C 199 LYS cc_start: 0.8531 (mttt) cc_final: 0.7880 (mmtm) REVERT: C 303 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7158 (tmm160) REVERT: C 311 LYS cc_start: 0.7822 (tptt) cc_final: 0.7231 (tmmt) REVERT: C 321 LYS cc_start: 0.7334 (mppt) cc_final: 0.7056 (mptp) REVERT: D 42 ARG cc_start: 0.6766 (mtp180) cc_final: 0.6331 (mmp80) REVERT: D 139 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7986 (ptpp) REVERT: D 199 LYS cc_start: 0.8505 (mttt) cc_final: 0.7856 (mmtm) REVERT: D 242 LYS cc_start: 0.8141 (mttm) cc_final: 0.7647 (mmmm) REVERT: D 311 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7247 (tmmt) REVERT: D 321 LYS cc_start: 0.7383 (mppt) cc_final: 0.7073 (mptp) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 0.9074 time to fit residues: 90.9198 Evaluate side-chains 89 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 35 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099306 restraints weight = 10580.531| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.35 r_work: 0.2934 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10672 Z= 0.153 Angle : 0.557 6.208 14464 Z= 0.293 Chirality : 0.044 0.154 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.507 54.368 1484 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.16 % Allowed : 7.91 % Favored : 89.93 % 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: 1.73 (0.23), residues: 1364 helix: 2.62 (0.19), residues: 712 sheet: -1.15 (0.32), residues: 252 loop : 0.11 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 59 TYR 0.025 0.002 TYR B 213 PHE 0.015 0.002 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00336 (10672) covalent geometry : angle 0.55699 (14464) hydrogen bonds : bond 0.06113 ( 587) hydrogen bonds : angle 4.61059 ( 1695) *********************** 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 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.407 Fit side-chains REVERT: A 42 ARG cc_start: 0.6709 (mtp180) cc_final: 0.6335 (mmp80) REVERT: A 52 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: A 139 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7988 (ptpp) REVERT: A 199 LYS cc_start: 0.8565 (mttt) cc_final: 0.7926 (mmtm) REVERT: A 311 LYS cc_start: 0.7946 (ttmm) cc_final: 0.7312 (tmmt) REVERT: A 321 LYS cc_start: 0.7431 (mppt) cc_final: 0.7105 (mptp) REVERT: B 42 ARG cc_start: 0.6826 (mtp180) cc_final: 0.6388 (mmp80) REVERT: B 52 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: B 199 LYS cc_start: 0.8562 (mttt) cc_final: 0.7916 (mmtm) REVERT: B 311 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7358 (tmmt) REVERT: C 42 ARG cc_start: 0.6468 (mtp180) cc_final: 0.6144 (mmp80) REVERT: C 52 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: C 139 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7978 (ptpp) REVERT: C 146 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8508 (ttmt) REVERT: C 199 LYS cc_start: 0.8573 (mttt) cc_final: 0.7908 (mmtm) REVERT: C 303 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7210 (tmm160) REVERT: C 311 LYS cc_start: 0.7880 (tptt) cc_final: 0.7278 (tmmt) REVERT: C 321 LYS cc_start: 0.7411 (mppt) cc_final: 0.7088 (mptp) REVERT: D 42 ARG cc_start: 0.6729 (mtp180) cc_final: 0.6325 (mmp80) REVERT: D 199 LYS cc_start: 0.8546 (mttt) cc_final: 0.7883 (mmtm) REVERT: D 242 LYS cc_start: 0.8156 (mttm) cc_final: 0.7649 (mmmm) REVERT: D 311 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7366 (tmmt) REVERT: D 321 LYS cc_start: 0.7404 (mppt) cc_final: 0.7084 (mptp) outliers start: 24 outliers final: 11 residues processed: 101 average time/residue: 0.8747 time to fit residues: 93.4560 Evaluate side-chains 90 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098923 restraints weight = 10549.172| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.34 r_work: 0.2934 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.155 Angle : 0.565 6.708 14464 Z= 0.297 Chirality : 0.044 0.153 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.544 53.667 1484 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.62 % Allowed : 8.45 % Favored : 89.93 % 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: 1.64 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 712 sheet: -1.24 (0.32), residues: 252 loop : 0.06 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 200 TYR 0.025 0.002 TYR C 213 PHE 0.016 0.002 PHE C 144 TRP 0.012 0.002 TRP A 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00342 (10672) covalent geometry : angle 0.56527 (14464) hydrogen bonds : bond 0.06189 ( 587) hydrogen bonds : angle 4.66633 ( 1695) *********************** 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 96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.448 Fit side-chains REVERT: A 42 ARG cc_start: 0.6730 (mtp180) cc_final: 0.6347 (mmp80) REVERT: A 52 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6745 (tp30) REVERT: A 199 LYS cc_start: 0.8553 (mttt) cc_final: 0.7919 (mmtm) REVERT: A 311 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7312 (tmmt) REVERT: A 321 LYS cc_start: 0.7445 (mppt) cc_final: 0.7109 (mptp) REVERT: B 42 ARG cc_start: 0.6825 (mtp180) cc_final: 0.6388 (mmp80) REVERT: B 52 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7163 (tp30) REVERT: B 199 LYS cc_start: 0.8557 (mttt) cc_final: 0.7918 (mmtm) REVERT: B 311 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7354 (tmmt) REVERT: C 42 ARG cc_start: 0.6491 (mtp180) cc_final: 0.6151 (mmp80) REVERT: C 52 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: C 199 LYS cc_start: 0.8577 (mttt) cc_final: 0.7911 (mmtm) REVERT: C 303 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7064 (mtm-85) REVERT: C 311 LYS cc_start: 0.7898 (tptt) cc_final: 0.7353 (tmmt) REVERT: C 321 LYS cc_start: 0.7404 (mppt) cc_final: 0.7090 (mptp) REVERT: D 42 ARG cc_start: 0.6733 (mtp180) cc_final: 0.6258 (mmp80) REVERT: D 199 LYS cc_start: 0.8545 (mttt) cc_final: 0.7889 (mmtm) REVERT: D 242 LYS cc_start: 0.8150 (mttm) cc_final: 0.7636 (mmmm) REVERT: D 311 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7374 (tmmt) REVERT: D 321 LYS cc_start: 0.7426 (mppt) cc_final: 0.7096 (mptp) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.8725 time to fit residues: 87.7046 Evaluate side-chains 87 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 114 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099649 restraints weight = 10342.007| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.35 r_work: 0.2971 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.131 Angle : 0.531 7.092 14464 Z= 0.278 Chirality : 0.042 0.148 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.425 53.715 1484 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 8.90 % Favored : 89.66 % 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: 1.77 (0.23), residues: 1364 helix: 2.67 (0.19), residues: 712 sheet: -1.20 (0.32), residues: 252 loop : 0.11 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.022 0.002 TYR B 213 PHE 0.015 0.002 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00282 (10672) covalent geometry : angle 0.53135 (14464) hydrogen bonds : bond 0.05580 ( 587) hydrogen bonds : angle 4.56897 ( 1695) *********************** 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 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.505 Fit side-chains REVERT: A 42 ARG cc_start: 0.6755 (mtp180) cc_final: 0.6410 (mmp80) REVERT: A 52 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: A 199 LYS cc_start: 0.8550 (mttt) cc_final: 0.7917 (mmtm) REVERT: A 247 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 311 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7317 (tmmt) REVERT: A 321 LYS cc_start: 0.7416 (mppt) cc_final: 0.7097 (mptp) REVERT: B 42 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6461 (mmp80) REVERT: B 52 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: B 199 LYS cc_start: 0.8550 (mttt) cc_final: 0.7912 (mmtm) REVERT: B 311 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7387 (tmmt) REVERT: B 321 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7366 (mppt) REVERT: C 42 ARG cc_start: 0.6525 (mtp180) cc_final: 0.6215 (mmp80) REVERT: C 52 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6820 (tp30) REVERT: C 146 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8515 (ttmt) REVERT: C 199 LYS cc_start: 0.8568 (mttt) cc_final: 0.7908 (mmtm) REVERT: C 303 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7202 (tmm160) REVERT: C 311 LYS cc_start: 0.7887 (tptt) cc_final: 0.7287 (tmmt) REVERT: C 321 LYS cc_start: 0.7393 (mppt) cc_final: 0.7117 (mptp) REVERT: D 42 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6382 (mmp80) REVERT: D 52 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: D 199 LYS cc_start: 0.8528 (mttt) cc_final: 0.7882 (mmtm) REVERT: D 242 LYS cc_start: 0.8174 (mttm) cc_final: 0.7666 (mmmm) REVERT: D 311 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7303 (tmmt) REVERT: D 321 LYS cc_start: 0.7398 (mppt) cc_final: 0.7086 (mptp) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 1.0353 time to fit residues: 100.4065 Evaluate side-chains 89 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 113 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100522 restraints weight = 10518.872| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.36 r_work: 0.2961 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10672 Z= 0.118 Angle : 0.509 7.440 14464 Z= 0.265 Chirality : 0.041 0.145 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.323 53.810 1484 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.35 % Allowed : 8.90 % Favored : 89.75 % 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: 1.86 (0.23), residues: 1364 helix: 2.76 (0.19), residues: 712 sheet: -1.16 (0.32), residues: 252 loop : 0.15 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.020 0.002 TYR B 213 PHE 0.015 0.001 PHE C 144 TRP 0.011 0.002 TRP B 147 HIS 0.003 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00250 (10672) covalent geometry : angle 0.50893 (14464) hydrogen bonds : bond 0.05156 ( 587) hydrogen bonds : angle 4.48590 ( 1695) ********************** 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 91 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.451 Fit side-chains REVERT: A 42 ARG cc_start: 0.6630 (mtp180) cc_final: 0.6377 (mmp80) REVERT: A 52 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6769 (tp30) REVERT: A 199 LYS cc_start: 0.8508 (mttt) cc_final: 0.7859 (mmtm) REVERT: A 247 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 311 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7279 (tmmt) REVERT: A 321 LYS cc_start: 0.7362 (mppt) cc_final: 0.7046 (mptp) REVERT: B 42 ARG cc_start: 0.6834 (mtp180) cc_final: 0.6429 (mmp80) REVERT: B 52 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: B 199 LYS cc_start: 0.8505 (mttt) cc_final: 0.7852 (mmtm) REVERT: B 311 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7323 (tmmt) REVERT: B 321 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7318 (mppt) REVERT: C 42 ARG cc_start: 0.6490 (mtp180) cc_final: 0.6180 (mmp80) REVERT: C 52 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: C 199 LYS cc_start: 0.8539 (mttt) cc_final: 0.7861 (mmtm) REVERT: C 303 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7142 (tmm160) REVERT: C 311 LYS cc_start: 0.7817 (tptt) cc_final: 0.7204 (tmmt) REVERT: C 321 LYS cc_start: 0.7344 (mppt) cc_final: 0.7075 (mptp) REVERT: D 42 ARG cc_start: 0.6715 (mtp180) cc_final: 0.6335 (mmp80) REVERT: D 52 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6892 (tp30) REVERT: D 199 LYS cc_start: 0.8506 (mttt) cc_final: 0.7838 (mmtm) REVERT: D 242 LYS cc_start: 0.8154 (mttm) cc_final: 0.7639 (mmmm) REVERT: D 311 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7256 (tmmt) REVERT: D 321 LYS cc_start: 0.7340 (mppt) cc_final: 0.7030 (mptp) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.9705 time to fit residues: 92.1852 Evaluate side-chains 88 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 85 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.097880 restraints weight = 10431.976| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.36 r_work: 0.2930 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10672 Z= 0.173 Angle : 0.591 7.645 14464 Z= 0.310 Chirality : 0.045 0.157 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.590 52.705 1484 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 8.81 % Favored : 89.75 % 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: 1.59 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 708 sheet: -1.71 (0.35), residues: 204 loop : 0.06 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 200 TYR 0.027 0.002 TYR B 213 PHE 0.015 0.002 PHE C 144 TRP 0.013 0.003 TRP B 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00388 (10672) covalent geometry : angle 0.59069 (14464) hydrogen bonds : bond 0.06533 ( 587) hydrogen bonds : angle 4.70133 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.61 seconds wall clock time: 77 minutes 49.00 seconds (4669.00 seconds total)