Starting phenix.real_space_refine on Sun May 3 07:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nh_75860/05_2026/11nh_75860.map" } resolution = 2.42 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= 0.006 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 3011 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: 11503 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: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 244 Classifications: {'water': 244} Link IDs: {None: 243} Chain: "B" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 281 Classifications: {'water': 281} Link IDs: {None: 280} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "D" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 268 Classifications: {'water': 268} Link IDs: {None: 267} Time building chain proxies: 3.13, per 1000 atoms: 0.27 Number of scatterers: 11503 At special positions: 0 Unit cell: (99.96, 80.115, 108.045, 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 3011 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: 1.02 Conformation dependent library (CDL) restraints added in 651.0 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: 60 helices and 8 sheets defined 55.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.797A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.935A 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: 3.977A 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 removed outlier: 3.580A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.527A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.239A 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: 3.569A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.806A 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 85 removed outlier: 3.807A 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 141 Processing helix chain 'B' and resid 159 through 180 removed outlier: 3.552A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 275 through 288 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 47 removed outlier: 3.734A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.001A 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: 3.834A 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 141 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 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.138A 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 removed outlier: 3.529A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.683A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (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: 3.912A 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 removed outlier: 3.561A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 275 through 288 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 31 removed outlier: 5.542A pdb=" N GLY A 28 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU A 270 " --> pdb=" O LEU A 228 " (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: 6.722A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP B 143 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.267A 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: 6.415A pdb=" N GLY C 28 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE C 77 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU C 30 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 301 " --> pdb=" O ILE C 29 " (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: 6.714A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 578 hydrogen bonds defined for protein. 1677 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: 2.01 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1780 1.31 - 1.44: 2585 1.44 - 1.56: 6248 1.56 - 1.69: 3 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C LYS A 317 " pdb=" O LYS A 317 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.17e-02 7.31e+03 1.70e+01 bond pdb=" C LYS B 293 " pdb=" N PRO B 294 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.06e+00 bond pdb=" N TRP B 147 " pdb=" CA TRP B 147 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.24e-02 6.50e+03 8.69e+00 bond pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.00e-02 1.00e+04 8.67e+00 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.43e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 14178 2.36 - 4.73: 257 4.73 - 7.09: 27 7.09 - 9.45: 1 9.45 - 11.81: 1 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 113.80 118.44 -4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.26 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 117.81 -4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA LYS A 317 " pdb=" C LYS A 317 " pdb=" O LYS A 317 " ideal model delta sigma weight residual 120.55 116.32 4.23 1.06e+00 8.90e-01 1.59e+01 angle pdb=" CA THR D 298 " pdb=" CB THR D 298 " pdb=" OG1 THR D 298 " ideal model delta sigma weight residual 109.60 103.68 5.92 1.50e+00 4.44e-01 1.56e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6048 17.87 - 35.74: 354 35.74 - 53.61: 66 53.61 - 71.48: 24 71.48 - 89.35: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" C PHE B 144 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " ideal model delta harmonic sigma weight residual -122.60 -132.14 9.54 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C PHE C 144 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " ideal model delta harmonic sigma weight residual -122.60 -131.55 8.95 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C THR C 298 " pdb=" N THR C 298 " pdb=" CA THR C 298 " pdb=" CB THR C 298 " ideal model delta harmonic sigma weight residual -122.00 -130.32 8.32 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 1623 0.157 - 0.313: 20 0.313 - 0.470: 0 0.470 - 0.627: 0 0.627 - 0.783: 1 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CG LEU A 320 " pdb=" CB LEU A 320 " pdb=" CD1 LEU A 320 " pdb=" CD2 LEU A 320 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PHE C 144 " pdb=" N PHE C 144 " pdb=" C PHE C 144 " pdb=" CB PHE C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 298 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C THR D 298 " -0.045 2.00e-02 2.50e+03 pdb=" O THR D 298 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE D 299 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 317 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C LYS A 317 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 317 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 318 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 326 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C GLU B 326 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU B 326 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 327 " -0.013 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2505 2.78 - 3.31: 11554 3.31 - 3.84: 21916 3.84 - 4.37: 27114 4.37 - 4.90: 42483 Nonbonded interactions: 105572 Sorted by model distance: nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.246 3.040 nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.280 3.040 nonbonded pdb=" O GLU A 155 " pdb=" NE2 HIS B 2 " model vdw 2.299 3.120 nonbonded pdb=" OE2 GLU D 81 " pdb=" O HOH D 401 " model vdw 2.302 3.040 nonbonded pdb=" OD2 ASP B 66 " pdb=" O HOH B 401 " model vdw 2.307 3.040 ... (remaining 105567 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: 5.620 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 0.091 10672 Z= 0.299 Angle : 0.799 11.813 14464 Z= 0.482 Chirality : 0.055 0.783 1644 Planarity : 0.006 0.055 1880 Dihedral : 12.923 89.346 3984 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.08 % Allowed : 0.54 % Favored : 98.38 % 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: 1.14 (0.23), residues: 1364 helix: 1.55 (0.19), residues: 712 sheet: -1.16 (0.37), residues: 184 loop : 0.54 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG D 257 TYR 0.023 0.002 TYR B 213 PHE 0.024 0.003 PHE B 144 TRP 0.030 0.005 TRP C 147 HIS 0.009 0.003 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00528 (10672) covalent geometry : angle 0.79902 (14464) hydrogen bonds : bond 0.15058 ( 578) hydrogen bonds : angle 5.87344 ( 1677) *********************** 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 213 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.418 Fit side-chains REVERT: A 139 LYS cc_start: 0.8106 (ptmt) cc_final: 0.7862 (ptpt) REVERT: A 193 ASP cc_start: 0.8132 (m-30) cc_final: 0.7923 (m-30) REVERT: A 206 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8216 (mt-10) REVERT: A 242 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6971 (mmtt) REVERT: A 277 GLU cc_start: 0.7205 (tp30) cc_final: 0.6996 (tp30) REVERT: B 152 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7699 (pttt) REVERT: B 199 LYS cc_start: 0.7642 (ttpp) cc_final: 0.7429 (mmpt) REVERT: B 303 ARG cc_start: 0.7442 (ttm110) cc_final: 0.6424 (ttp80) REVERT: B 311 LYS cc_start: 0.7382 (mmtp) cc_final: 0.6935 (ttpp) REVERT: C 278 GLU cc_start: 0.7927 (tt0) cc_final: 0.7650 (tp30) REVERT: D 95 GLN cc_start: 0.7981 (tt0) cc_final: 0.7771 (mt0) REVERT: D 152 LYS cc_start: 0.8365 (pttt) cc_final: 0.7796 (ptpt) REVERT: D 237 HIS cc_start: 0.7527 (t-90) cc_final: 0.7240 (m90) REVERT: D 311 LYS cc_start: 0.7983 (tttp) cc_final: 0.7399 (ttpt) REVERT: D 321 LYS cc_start: 0.7166 (tptt) cc_final: 0.6832 (mmmt) outliers start: 12 outliers final: 2 residues processed: 209 average time/residue: 0.8752 time to fit residues: 193.1242 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B 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: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 85 GLN A 166 ASN A 168 ASN A 241 GLN A 274 GLN B 274 GLN C 2 HIS C 95 GLN C 119 ASN C 180 ASN D 60 GLN D 241 GLN D 319 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117000 restraints weight = 10797.599| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.48 r_work: 0.3226 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10672 Z= 0.118 Angle : 0.502 5.533 14464 Z= 0.268 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.038 1880 Dihedral : 4.558 58.409 1476 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 6.47 % Favored : 91.10 % 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: 2.11 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 712 sheet: -0.60 (0.34), residues: 232 loop : 0.73 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 330 TYR 0.021 0.002 TYR C 213 PHE 0.011 0.001 PHE D 144 TRP 0.017 0.002 TRP C 147 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00261 (10672) covalent geometry : angle 0.50243 (14464) hydrogen bonds : bond 0.04611 ( 578) hydrogen bonds : angle 4.22133 ( 1677) *********************** 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 144 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.451 Fit side-chains REVERT: A 14 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7303 (pp20) REVERT: A 86 LYS cc_start: 0.7461 (mtpp) cc_final: 0.6886 (mtmt) REVERT: A 95 GLN cc_start: 0.6498 (tt0) cc_final: 0.5779 (tp-100) REVERT: A 139 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7236 (ptpt) REVERT: A 164 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7573 (tmm) REVERT: A 193 ASP cc_start: 0.7916 (m-30) cc_final: 0.7651 (m-30) REVERT: A 206 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 107 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8610 (ttmm) REVERT: B 199 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7456 (mmpt) REVERT: B 303 ARG cc_start: 0.7805 (ttm110) cc_final: 0.6653 (ttp80) REVERT: B 311 LYS cc_start: 0.7596 (mmtp) cc_final: 0.7074 (ttpp) REVERT: C 155 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6205 (pt0) REVERT: C 295 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.7799 (m-90) REVERT: C 303 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.6292 (mtm-85) REVERT: D 152 LYS cc_start: 0.8327 (pttt) cc_final: 0.7495 (ptpt) REVERT: D 237 HIS cc_start: 0.7532 (t-90) cc_final: 0.7028 (m170) REVERT: D 292 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7611 (tt) REVERT: D 311 LYS cc_start: 0.7839 (tttp) cc_final: 0.7241 (ttpt) REVERT: D 325 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6955 (tp30) outliers start: 27 outliers final: 7 residues processed: 134 average time/residue: 0.8727 time to fit residues: 123.6576 Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 241 GLN C 4 HIS C 60 GLN C 95 GLN D 60 GLN D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110628 restraints weight = 10833.646| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.48 r_work: 0.3142 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2138 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= 0.131 Angle : 0.512 5.249 14464 Z= 0.274 Chirality : 0.041 0.159 1644 Planarity : 0.004 0.037 1880 Dihedral : 4.748 59.346 1476 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.25 % Allowed : 7.82 % 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: 2.17 (0.23), residues: 1364 helix: 2.63 (0.19), residues: 712 sheet: -0.21 (0.38), residues: 176 loop : 0.32 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 59 TYR 0.026 0.002 TYR C 213 PHE 0.014 0.002 PHE D 144 TRP 0.019 0.002 TRP D 147 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00295 (10672) covalent geometry : angle 0.51155 (14464) hydrogen bonds : bond 0.05196 ( 578) hydrogen bonds : angle 4.10834 ( 1677) *********************** 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 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.431 Fit side-chains REVERT: A 14 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: A 86 LYS cc_start: 0.7617 (mtpp) cc_final: 0.6995 (mttt) REVERT: A 95 GLN cc_start: 0.6463 (tt0) cc_final: 0.5777 (tp-100) REVERT: A 139 LYS cc_start: 0.8018 (ptmt) cc_final: 0.7333 (ptpt) REVERT: A 164 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7568 (tmm) REVERT: A 193 ASP cc_start: 0.7926 (m-30) cc_final: 0.7622 (m-30) REVERT: A 242 LYS cc_start: 0.7305 (mmtm) cc_final: 0.6660 (mmtt) REVERT: B 107 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (ttmm) REVERT: B 303 ARG cc_start: 0.7864 (ttm110) cc_final: 0.6736 (ttp80) REVERT: B 311 LYS cc_start: 0.7755 (mmtp) cc_final: 0.7170 (ttpp) REVERT: B 321 LYS cc_start: 0.7316 (mmmt) cc_final: 0.6348 (tmtt) REVERT: C 2 HIS cc_start: 0.4381 (OUTLIER) cc_final: 0.4100 (m-70) REVERT: C 278 GLU cc_start: 0.7849 (tt0) cc_final: 0.7118 (tp30) REVERT: C 295 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.7804 (m-90) REVERT: D 152 LYS cc_start: 0.8393 (pttt) cc_final: 0.7408 (pmmt) REVERT: D 237 HIS cc_start: 0.7573 (t-90) cc_final: 0.7039 (m90) REVERT: D 295 TRP cc_start: 0.8592 (OUTLIER) cc_final: 0.7702 (m-90) REVERT: D 303 ARG cc_start: 0.7740 (ptp-170) cc_final: 0.6331 (ptt180) REVERT: D 311 LYS cc_start: 0.7899 (tttp) cc_final: 0.7288 (ttpt) REVERT: D 325 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6974 (tp30) outliers start: 25 outliers final: 6 residues processed: 122 average time/residue: 0.8724 time to fit residues: 112.6484 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 120 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 339 GLN B 119 ASN C 95 GLN C 168 ASN D 60 GLN D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110839 restraints weight = 10907.346| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.47 r_work: 0.3159 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10672 Z= 0.116 Angle : 0.488 9.145 14464 Z= 0.257 Chirality : 0.040 0.152 1644 Planarity : 0.004 0.039 1880 Dihedral : 4.637 59.222 1476 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.61 % Allowed : 8.27 % 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: 2.22 (0.23), residues: 1364 helix: 2.72 (0.19), residues: 712 sheet: -0.31 (0.38), residues: 176 loop : 0.30 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 91 TYR 0.021 0.002 TYR C 213 PHE 0.015 0.001 PHE D 144 TRP 0.017 0.002 TRP D 147 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00264 (10672) covalent geometry : angle 0.48764 (14464) hydrogen bonds : bond 0.04680 ( 578) hydrogen bonds : angle 4.01937 ( 1677) *********************** 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 130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.379 Fit side-chains REVERT: A 14 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: A 86 LYS cc_start: 0.7661 (mtpp) cc_final: 0.7027 (mttt) REVERT: A 95 GLN cc_start: 0.6465 (tt0) cc_final: 0.5783 (tp-100) REVERT: A 98 LYS cc_start: 0.6858 (mttp) cc_final: 0.6623 (mmtp) REVERT: A 139 LYS cc_start: 0.8073 (ptmt) cc_final: 0.7367 (ptpt) REVERT: A 164 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7536 (tmm) REVERT: A 193 ASP cc_start: 0.7882 (m-30) cc_final: 0.7603 (m-30) REVERT: A 206 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 242 LYS cc_start: 0.7273 (mmtm) cc_final: 0.6613 (mmtt) REVERT: B 107 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8599 (ttmm) REVERT: B 199 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7483 (mmpt) REVERT: B 303 ARG cc_start: 0.7788 (ttm110) cc_final: 0.6653 (ttp80) REVERT: B 311 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7162 (ttpp) REVERT: C 2 HIS cc_start: 0.4364 (OUTLIER) cc_final: 0.4049 (m-70) REVERT: C 52 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6325 (tp30) REVERT: C 278 GLU cc_start: 0.7823 (tt0) cc_final: 0.7109 (tp30) REVERT: C 295 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.7713 (m-90) REVERT: D 152 LYS cc_start: 0.8426 (pttt) cc_final: 0.7578 (ptpt) REVERT: D 237 HIS cc_start: 0.7619 (t-90) cc_final: 0.7069 (m90) REVERT: D 295 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7587 (m-90) REVERT: D 311 LYS cc_start: 0.7928 (tttp) cc_final: 0.7363 (ttpt) REVERT: D 325 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7013 (tp30) outliers start: 29 outliers final: 9 residues processed: 123 average time/residue: 0.8085 time to fit residues: 105.7144 Evaluate side-chains 112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 132 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 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 119 ASN C 54 ASN C 95 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106123 restraints weight = 10884.987| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.47 r_work: 0.3093 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10672 Z= 0.177 Angle : 0.564 6.054 14464 Z= 0.300 Chirality : 0.044 0.176 1644 Planarity : 0.004 0.040 1880 Dihedral : 4.989 55.264 1476 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.70 % Allowed : 8.27 % 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: 1.92 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 712 sheet: -0.99 (0.40), residues: 144 loop : 0.29 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.030 0.002 TYR A 213 PHE 0.018 0.002 PHE D 144 TRP 0.023 0.003 TRP D 147 HIS 0.008 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00419 (10672) covalent geometry : angle 0.56364 (14464) hydrogen bonds : bond 0.06045 ( 578) hydrogen bonds : angle 4.23354 ( 1677) *********************** 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 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.359 Fit side-chains REVERT: A 14 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: A 95 GLN cc_start: 0.6372 (tt0) cc_final: 0.5711 (tp-100) REVERT: A 139 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7539 (ptpt) REVERT: A 152 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7022 (ptpt) REVERT: A 164 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7588 (tmm) REVERT: A 193 ASP cc_start: 0.7882 (m-30) cc_final: 0.7576 (m-30) REVERT: A 206 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 242 LYS cc_start: 0.7345 (mmtm) cc_final: 0.6566 (mmtt) REVERT: A 329 LYS cc_start: 0.5791 (mtpt) cc_final: 0.5042 (ptmm) REVERT: B 107 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8652 (ttmm) REVERT: B 189 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: B 270 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8120 (pp) REVERT: B 303 ARG cc_start: 0.7897 (ttm110) cc_final: 0.6743 (ttp80) REVERT: B 311 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7257 (ttpp) REVERT: C 2 HIS cc_start: 0.4508 (OUTLIER) cc_final: 0.4047 (m-70) REVERT: C 278 GLU cc_start: 0.7812 (tt0) cc_final: 0.7142 (tp30) REVERT: C 295 TRP cc_start: 0.8599 (OUTLIER) cc_final: 0.7775 (m-90) REVERT: D 152 LYS cc_start: 0.8473 (pttt) cc_final: 0.7490 (pmmt) REVERT: D 237 HIS cc_start: 0.7625 (t-90) cc_final: 0.7028 (m170) REVERT: D 295 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.7679 (m-90) REVERT: D 311 LYS cc_start: 0.8003 (tttp) cc_final: 0.7399 (ttpt) REVERT: D 317 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7296 (ttmt) REVERT: D 325 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7072 (tp30) outliers start: 30 outliers final: 10 residues processed: 121 average time/residue: 0.8423 time to fit residues: 108.1280 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 95 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 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 = 0.3708 r_free = 0.3708 target = 0.147693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110851 restraints weight = 10894.376| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.47 r_work: 0.3160 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10672 Z= 0.106 Angle : 0.466 5.100 14464 Z= 0.246 Chirality : 0.040 0.142 1644 Planarity : 0.004 0.037 1880 Dihedral : 4.590 55.905 1476 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.79 % Allowed : 8.63 % Favored : 88.58 % 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: 2.16 (0.23), residues: 1364 helix: 2.74 (0.19), residues: 712 sheet: -0.54 (0.37), residues: 176 loop : 0.24 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 42 TYR 0.018 0.002 TYR C 213 PHE 0.015 0.001 PHE D 144 TRP 0.013 0.001 TRP D 147 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00236 (10672) covalent geometry : angle 0.46576 (14464) hydrogen bonds : bond 0.04456 ( 578) hydrogen bonds : angle 3.99390 ( 1677) *********************** 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 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.448 Fit side-chains REVERT: A 14 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: A 95 GLN cc_start: 0.6384 (tt0) cc_final: 0.5713 (tp-100) REVERT: A 139 LYS cc_start: 0.8130 (ptmt) cc_final: 0.7404 (ptpt) REVERT: A 152 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7474 (ptpt) REVERT: A 164 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7508 (tmm) REVERT: A 193 ASP cc_start: 0.7828 (m-30) cc_final: 0.7566 (m-30) REVERT: A 206 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 242 LYS cc_start: 0.7384 (mmtm) cc_final: 0.6628 (mmtt) REVERT: A 295 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.5520 (m-90) REVERT: A 329 LYS cc_start: 0.5754 (mtpt) cc_final: 0.5012 (ptmm) REVERT: B 107 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: B 189 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: B 303 ARG cc_start: 0.7761 (ttm110) cc_final: 0.6611 (ttp80) REVERT: B 311 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7207 (ttpp) REVERT: C 2 HIS cc_start: 0.4446 (OUTLIER) cc_final: 0.4029 (m-70) REVERT: C 52 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6288 (tp30) REVERT: C 278 GLU cc_start: 0.7812 (tt0) cc_final: 0.7132 (tp30) REVERT: C 295 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.7646 (m-90) REVERT: D 152 LYS cc_start: 0.8474 (pttt) cc_final: 0.7592 (ptpt) REVERT: D 237 HIS cc_start: 0.7621 (t-90) cc_final: 0.7050 (m170) REVERT: D 295 TRP cc_start: 0.8507 (OUTLIER) cc_final: 0.7437 (m-90) REVERT: D 311 LYS cc_start: 0.7908 (tttp) cc_final: 0.7327 (ttpt) REVERT: D 325 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7054 (tp30) outliers start: 31 outliers final: 9 residues processed: 121 average time/residue: 0.8407 time to fit residues: 107.7690 Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 339 GLN C 95 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 241 GLN D 319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109125 restraints weight = 10957.130| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.47 r_work: 0.3135 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.124 Angle : 0.488 5.047 14464 Z= 0.258 Chirality : 0.041 0.154 1644 Planarity : 0.004 0.036 1880 Dihedral : 4.642 55.259 1476 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.43 % Allowed : 8.99 % Favored : 88.58 % 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: 2.06 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 720 sheet: -0.55 (0.37), residues: 176 loop : 0.15 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.023 0.002 TYR A 213 PHE 0.016 0.001 PHE D 144 TRP 0.016 0.002 TRP D 147 HIS 0.007 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00284 (10672) covalent geometry : angle 0.48775 (14464) hydrogen bonds : bond 0.04879 ( 578) hydrogen bonds : angle 4.00906 ( 1677) *********************** 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 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.442 Fit side-chains REVERT: A 14 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: A 95 GLN cc_start: 0.6377 (tt0) cc_final: 0.5737 (tp-100) REVERT: A 139 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7550 (ptpt) REVERT: A 152 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.6994 (ptpt) REVERT: A 164 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7534 (tmm) REVERT: A 193 ASP cc_start: 0.7854 (m-30) cc_final: 0.7579 (m-30) REVERT: A 206 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 242 LYS cc_start: 0.7345 (mmtm) cc_final: 0.6572 (mmtt) REVERT: A 295 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.5495 (m-90) REVERT: A 329 LYS cc_start: 0.5772 (mtpt) cc_final: 0.5032 (ptmm) REVERT: B 107 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: B 189 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 270 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8127 (pp) REVERT: B 303 ARG cc_start: 0.7839 (ttm110) cc_final: 0.6710 (ttp80) REVERT: B 311 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7174 (ttpp) REVERT: B 317 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7518 (mttm) REVERT: C 2 HIS cc_start: 0.4500 (OUTLIER) cc_final: 0.4045 (m-70) REVERT: C 52 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6269 (tp30) REVERT: C 278 GLU cc_start: 0.7821 (tt0) cc_final: 0.7127 (tp30) REVERT: C 295 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7779 (m-90) REVERT: D 152 LYS cc_start: 0.8491 (pttt) cc_final: 0.7603 (ptpt) REVERT: D 237 HIS cc_start: 0.7605 (t-90) cc_final: 0.7035 (m170) REVERT: D 295 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.7487 (m-90) REVERT: D 311 LYS cc_start: 0.7915 (tttp) cc_final: 0.7342 (ttpt) REVERT: D 325 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7042 (tp30) outliers start: 27 outliers final: 7 residues processed: 113 average time/residue: 0.8505 time to fit residues: 101.7580 Evaluate side-chains 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 37 optimal weight: 0.0020 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 339 GLN C 95 GLN C 156 HIS D 60 GLN D 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114226 restraints weight = 10871.974| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.43 r_work: 0.3186 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10672 Z= 0.097 Angle : 0.445 4.992 14464 Z= 0.233 Chirality : 0.039 0.132 1644 Planarity : 0.004 0.037 1880 Dihedral : 4.400 55.944 1476 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.07 % Allowed : 9.62 % Favored : 88.31 % 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: 2.21 (0.23), residues: 1364 helix: 2.81 (0.19), residues: 720 sheet: -0.70 (0.36), residues: 196 loop : 0.32 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 42 TYR 0.016 0.001 TYR C 213 PHE 0.014 0.001 PHE D 144 TRP 0.012 0.001 TRP D 147 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00215 (10672) covalent geometry : angle 0.44490 (14464) hydrogen bonds : bond 0.04055 ( 578) hydrogen bonds : angle 3.85724 ( 1677) *********************** 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 120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.469 Fit side-chains REVERT: A 14 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7325 (pp20) REVERT: A 95 GLN cc_start: 0.6425 (tt0) cc_final: 0.5770 (tp-100) REVERT: A 139 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7570 (ptpt) REVERT: A 164 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7578 (tmm) REVERT: A 193 ASP cc_start: 0.7841 (m-30) cc_final: 0.7613 (m-30) REVERT: A 206 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 242 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6685 (mmtt) REVERT: A 295 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.5512 (m-90) REVERT: A 329 LYS cc_start: 0.5791 (mtpt) cc_final: 0.5070 (ptmm) REVERT: B 107 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8550 (ttmm) REVERT: B 189 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 303 ARG cc_start: 0.7764 (ttm110) cc_final: 0.6663 (ttp80) REVERT: B 311 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7218 (ttpp) REVERT: B 317 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7572 (mttm) REVERT: B 321 LYS cc_start: 0.7489 (mmmt) cc_final: 0.6350 (tmtt) REVERT: C 2 HIS cc_start: 0.4672 (OUTLIER) cc_final: 0.4269 (m-70) REVERT: C 52 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6341 (tp30) REVERT: C 139 LYS cc_start: 0.7767 (ptpt) cc_final: 0.6775 (mmtm) REVERT: C 278 GLU cc_start: 0.7840 (tt0) cc_final: 0.7184 (tp30) REVERT: C 295 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.7636 (m-90) REVERT: D 152 LYS cc_start: 0.8494 (pttt) cc_final: 0.7640 (ptpt) REVERT: D 237 HIS cc_start: 0.7637 (t-90) cc_final: 0.7153 (m90) REVERT: D 295 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.7436 (m-90) REVERT: D 311 LYS cc_start: 0.7898 (tttp) cc_final: 0.7352 (ttpt) REVERT: D 325 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7110 (tp30) outliers start: 23 outliers final: 5 residues processed: 115 average time/residue: 0.8574 time to fit residues: 104.4391 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.0060 chunk 10 optimal weight: 5.9990 chunk 117 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 241 GLN A 339 GLN C 95 GLN D 60 GLN D 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114584 restraints weight = 10784.270| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.46 r_work: 0.3212 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10672 Z= 0.091 Angle : 0.433 4.966 14464 Z= 0.225 Chirality : 0.038 0.128 1644 Planarity : 0.003 0.036 1880 Dihedral : 4.258 56.578 1476 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.98 % Allowed : 9.80 % Favored : 88.22 % 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: 2.28 (0.24), residues: 1364 helix: 2.91 (0.19), residues: 720 sheet: -0.99 (0.32), residues: 252 loop : 0.71 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 59 TYR 0.015 0.001 TYR A 213 PHE 0.013 0.001 PHE D 144 TRP 0.011 0.001 TRP D 147 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00202 (10672) covalent geometry : angle 0.43324 (14464) hydrogen bonds : bond 0.03746 ( 578) hydrogen bonds : angle 3.74479 ( 1677) *********************** 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 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.449 Fit side-chains REVERT: A 14 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: A 86 LYS cc_start: 0.7588 (mtpp) cc_final: 0.6939 (mttt) REVERT: A 95 GLN cc_start: 0.6369 (tt0) cc_final: 0.5723 (tp-100) REVERT: A 139 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7439 (ptpt) REVERT: A 152 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7467 (ptpt) REVERT: A 164 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7507 (tmm) REVERT: A 193 ASP cc_start: 0.7815 (m-30) cc_final: 0.7577 (m-30) REVERT: A 206 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 242 LYS cc_start: 0.7370 (mmtm) cc_final: 0.6623 (mmtt) REVERT: A 295 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.5403 (m-90) REVERT: A 329 LYS cc_start: 0.5691 (mtpt) cc_final: 0.4951 (ptmm) REVERT: B 189 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: B 303 ARG cc_start: 0.7747 (ttm110) cc_final: 0.6603 (ttp80) REVERT: B 311 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7095 (ttpp) REVERT: B 317 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7487 (mttm) REVERT: B 321 LYS cc_start: 0.7420 (mmmt) cc_final: 0.6274 (tmtt) REVERT: C 52 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6315 (tp30) REVERT: C 139 LYS cc_start: 0.7693 (ptpt) cc_final: 0.6714 (mmtm) REVERT: C 278 GLU cc_start: 0.7829 (tt0) cc_final: 0.7125 (tp30) REVERT: C 295 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7608 (m-90) REVERT: D 152 LYS cc_start: 0.8455 (pttt) cc_final: 0.7562 (ptpt) REVERT: D 237 HIS cc_start: 0.7633 (t-90) cc_final: 0.7153 (m90) REVERT: D 295 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7337 (m-90) REVERT: D 311 LYS cc_start: 0.7824 (tttp) cc_final: 0.7241 (ttpt) REVERT: D 325 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7012 (tp30) outliers start: 22 outliers final: 6 residues processed: 110 average time/residue: 0.8712 time to fit residues: 101.3878 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 241 GLN C 95 GLN D 60 GLN D 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110757 restraints weight = 10894.905| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.47 r_work: 0.3158 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.115 Angle : 0.472 4.873 14464 Z= 0.247 Chirality : 0.040 0.141 1644 Planarity : 0.004 0.035 1880 Dihedral : 4.465 55.367 1476 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.98 % Allowed : 10.07 % Favored : 87.95 % 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: 2.20 (0.23), residues: 1364 helix: 2.80 (0.19), residues: 720 sheet: -0.71 (0.36), residues: 196 loop : 0.32 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 42 TYR 0.024 0.002 TYR A 213 PHE 0.014 0.001 PHE D 144 TRP 0.015 0.002 TRP D 147 HIS 0.004 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00264 (10672) covalent geometry : angle 0.47163 (14464) hydrogen bonds : bond 0.04558 ( 578) hydrogen bonds : angle 3.85898 ( 1677) ********************** 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 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.462 Fit side-chains REVERT: A 14 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7305 (pp20) REVERT: A 95 GLN cc_start: 0.6391 (tt0) cc_final: 0.5730 (tp-100) REVERT: A 139 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7507 (ptpt) REVERT: A 152 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7466 (ptpt) REVERT: A 164 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: A 193 ASP cc_start: 0.7834 (m-30) cc_final: 0.7530 (m-30) REVERT: A 206 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8212 (mt-10) REVERT: A 242 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6616 (mmtt) REVERT: A 295 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.5449 (m-90) REVERT: A 329 LYS cc_start: 0.5723 (mtpt) cc_final: 0.4966 (ptmm) REVERT: B 189 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: B 303 ARG cc_start: 0.7789 (ttm110) cc_final: 0.6655 (ttp80) REVERT: B 311 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7126 (ttpp) REVERT: B 317 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7550 (mttm) REVERT: B 321 LYS cc_start: 0.7449 (mmmt) cc_final: 0.6296 (tmtt) REVERT: C 52 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6337 (tp30) REVERT: C 278 GLU cc_start: 0.7825 (tt0) cc_final: 0.7127 (tp30) REVERT: C 295 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.7737 (m-90) REVERT: D 152 LYS cc_start: 0.8468 (pttt) cc_final: 0.7579 (ptpt) REVERT: D 237 HIS cc_start: 0.7613 (t-90) cc_final: 0.7086 (m90) REVERT: D 295 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7451 (m-90) REVERT: D 311 LYS cc_start: 0.7884 (tttp) cc_final: 0.7293 (ttpt) REVERT: D 325 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7016 (tp30) outliers start: 22 outliers final: 6 residues processed: 111 average time/residue: 0.8343 time to fit residues: 98.1582 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 241 GLN A 339 GLN C 95 GLN D 60 GLN D 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110600 restraints weight = 10890.060| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.48 r_work: 0.3156 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.112 Angle : 0.470 4.959 14464 Z= 0.246 Chirality : 0.040 0.138 1644 Planarity : 0.004 0.036 1880 Dihedral : 4.478 55.122 1476 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 10.43 % Favored : 87.95 % 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: 2.21 (0.23), residues: 1364 helix: 2.78 (0.19), residues: 720 sheet: -0.55 (0.38), residues: 176 loop : 0.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 42 TYR 0.022 0.002 TYR A 213 PHE 0.015 0.001 PHE D 144 TRP 0.014 0.002 TRP D 147 HIS 0.004 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00256 (10672) covalent geometry : angle 0.46986 (14464) hydrogen bonds : bond 0.04514 ( 578) hydrogen bonds : angle 3.87915 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4547.55 seconds wall clock time: 78 minutes 17.31 seconds (4697.31 seconds total)