Starting phenix.real_space_refine on Wed Aug 5 09:55:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.cif Found real_map, /net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.map" model { file = "/net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27zv_81572/08_2026/27zv_81572.cif" } resolution = 3.0 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= 0.001 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 40 5.16 5 C 5940 2.51 5 N 1612 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9276 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "D" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Time building chain proxies: 2.26, per 1000 atoms: 0.24 Number of scatterers: 9276 At special positions: 0 Unit cell: (86.814, 86.814, 94.234, 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 40 16.00 O 1684 8.00 N 1612 7.00 C 5940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 319.3 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 26.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.558A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 86 through 102 removed outlier: 3.541A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 86 through 102 removed outlier: 3.559A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 Processing helix chain 'C' and resid 233 through 249 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 86 through 102 removed outlier: 3.557A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 269 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 15 through 24 current: chain 'C' and resid 37 through 51 removed outlier: 7.271A pdb=" N GLU C 42 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU C 114 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA C 44 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL C 112 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 46 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 110 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN C 48 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA C 108 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 50 " --> pdb=" O THR C 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 105 through 114 current: chain 'C' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 133 current: chain 'C' and resid 152 through 164 removed outlier: 4.805A pdb=" N ILE C 153 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP C 159 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 193 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 161 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 191 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 163 " --> pdb=" O PHE C 189 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE C 189 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 190 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN C 192 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 194 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 254 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HIS C 263 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N PHE C 265 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N ASP C 285 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS D 27 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU D 42 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 114 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA D 44 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 112 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER D 46 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 110 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN D 48 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA D 108 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 50 " --> pdb=" O THR D 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 105 through 114 current: chain 'D' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 133 current: chain 'D' and resid 152 through 164 removed outlier: 4.809A pdb=" N ILE D 153 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP D 159 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 193 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D 161 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR D 191 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 163 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE D 189 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA D 190 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN D 192 " --> pdb=" O PRO D 260 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 194 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP D 254 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N HIS D 263 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N PHE D 265 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ASP D 285 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 34 removed outlier: 7.265A pdb=" N GLU A 42 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 114 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 44 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 112 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER A 46 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 110 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN A 48 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 108 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 50 " --> pdb=" O THR A 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 105 through 114 current: chain 'A' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 133 current: chain 'A' and resid 152 through 158 removed outlier: 4.804A pdb=" N ILE A 153 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 194 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 254 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS A 263 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N PHE A 265 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N ASP A 285 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS B 27 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU B 42 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 114 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 44 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 112 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 46 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 110 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN B 48 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 108 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 50 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 139 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 153 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 159 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 193 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS B 161 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B 191 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 163 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 189 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 190 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 192 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 254 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS B 263 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N PHE B 265 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 10.283A pdb=" N ASP B 285 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 192 removed outlier: 5.711A pdb=" N LYS A 161 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N VAL B 128 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 12.464A pdb=" N LYS B 122 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA B 130 " --> pdb=" O PHE B 120 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3004 1.34 - 1.46: 1428 1.46 - 1.57: 5000 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9496 Sorted by residual: bond pdb=" CA ILE C 84 " pdb=" CB ILE C 84 " ideal model delta sigma weight residual 1.532 1.543 -0.011 1.08e-02 8.57e+03 9.67e-01 bond pdb=" CA ILE D 84 " pdb=" CB ILE D 84 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.08e-02 8.57e+03 8.93e-01 bond pdb=" CA ILE B 84 " pdb=" CB ILE B 84 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.08e-02 8.57e+03 8.62e-01 bond pdb=" CA ILE A 84 " pdb=" CB ILE A 84 " ideal model delta sigma weight residual 1.532 1.542 -0.010 1.08e-02 8.57e+03 8.57e-01 bond pdb=" CB MET B 272 " pdb=" CG MET B 272 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.15e-01 ... (remaining 9491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 12276 1.16 - 2.31: 452 2.31 - 3.47: 89 3.47 - 4.63: 11 4.63 - 5.78: 4 Bond angle restraints: 12832 Sorted by residual: angle pdb=" N ILE D 84 " pdb=" CA ILE D 84 " pdb=" C ILE D 84 " ideal model delta sigma weight residual 106.42 110.47 -4.05 1.51e+00 4.39e-01 7.20e+00 angle pdb=" N ILE A 84 " pdb=" CA ILE A 84 " pdb=" C ILE A 84 " ideal model delta sigma weight residual 106.42 110.47 -4.05 1.51e+00 4.39e-01 7.18e+00 angle pdb=" N ILE C 84 " pdb=" CA ILE C 84 " pdb=" C ILE C 84 " ideal model delta sigma weight residual 106.42 110.45 -4.03 1.51e+00 4.39e-01 7.14e+00 angle pdb=" N ILE B 84 " pdb=" CA ILE B 84 " pdb=" C ILE B 84 " ideal model delta sigma weight residual 106.42 110.45 -4.03 1.51e+00 4.39e-01 7.13e+00 angle pdb=" CA THR C 180 " pdb=" C THR C 180 " pdb=" O THR C 180 " ideal model delta sigma weight residual 120.27 123.40 -3.13 1.24e+00 6.50e-01 6.37e+00 ... (remaining 12827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 5112 14.56 - 29.12: 424 29.12 - 43.68: 147 43.68 - 58.25: 12 58.25 - 72.81: 9 Dihedral angle restraints: 5704 sinusoidal: 2380 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ASP C 56 " pdb=" C ASP C 56 " pdb=" N TYR C 57 " pdb=" CA TYR C 57 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASP A 56 " pdb=" C ASP A 56 " pdb=" N TYR A 57 " pdb=" CA TYR A 57 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASP B 56 " pdb=" C ASP B 56 " pdb=" N TYR B 57 " pdb=" CA TYR B 57 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 794 0.029 - 0.059: 399 0.059 - 0.088: 116 0.088 - 0.117: 86 0.117 - 0.147: 21 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CB THR A 180 " pdb=" CA THR A 180 " pdb=" OG1 THR A 180 " pdb=" CG2 THR A 180 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB THR B 180 " pdb=" CA THR B 180 " pdb=" OG1 THR B 180 " pdb=" CG2 THR B 180 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CB THR C 180 " pdb=" CA THR C 180 " pdb=" OG1 THR C 180 " pdb=" CG2 THR C 180 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1413 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 282 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO C 283 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 283 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 282 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 283 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " -0.022 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2868 2.84 - 3.35: 8254 3.35 - 3.87: 15117 3.87 - 4.38: 16698 4.38 - 4.90: 30184 Nonbonded interactions: 73121 Sorted by model distance: nonbonded pdb=" O VAL D 105 " pdb=" NH2 ARG D 147 " model vdw 2.322 3.120 nonbonded pdb=" O VAL A 105 " pdb=" NH2 ARG A 147 " model vdw 2.326 3.120 nonbonded pdb=" O VAL C 105 " pdb=" NH2 ARG C 147 " model vdw 2.327 3.120 nonbonded pdb=" O VAL B 105 " pdb=" NH2 ARG B 147 " model vdw 2.329 3.120 nonbonded pdb=" O ILE A 275 " pdb=" NZ LYS B 80 " model vdw 2.338 3.120 ... (remaining 73116 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.003 0.029 9496 Z= 0.131 Angle : 0.541 5.782 12832 Z= 0.314 Chirality : 0.044 0.147 1416 Planarity : 0.004 0.052 1632 Dihedral : 12.519 72.808 3560 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1132 helix: 2.94 (0.31), residues: 260 sheet: 0.94 (0.28), residues: 356 loop : -1.95 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 82 TYR 0.006 0.001 TYR A 57 PHE 0.015 0.001 PHE A 170 TRP 0.005 0.001 TRP A 117 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 9496) covalent geometry : angle 0.54137 / 0.31 (12832) hydrogen bonds : bond 0.11536 / 7.79 ( 347) hydrogen bonds : angle 6.66215 / 4.98 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.228 Fit side-chains REVERT: A 177 GLN cc_start: 0.8989 (pm20) cc_final: 0.8598 (pm20) REVERT: A 253 GLU cc_start: 0.8849 (tp30) cc_final: 0.8198 (tp30) REVERT: B 177 GLN cc_start: 0.8983 (pm20) cc_final: 0.8606 (pm20) REVERT: B 253 GLU cc_start: 0.8838 (tp30) cc_final: 0.8159 (tp30) REVERT: C 177 GLN cc_start: 0.8987 (pm20) cc_final: 0.8687 (pm20) REVERT: C 253 GLU cc_start: 0.8879 (tp30) cc_final: 0.8178 (tp30) REVERT: D 177 GLN cc_start: 0.8975 (pm20) cc_final: 0.8693 (pm20) REVERT: D 253 GLU cc_start: 0.8872 (tp30) cc_final: 0.8176 (tp30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.6438 time to fit residues: 122.6658 Evaluate side-chains 85 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A 97 HIS ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 97 HIS B 242 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.077229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.059439 restraints weight = 19289.760| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.68 r_work: 0.2646 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 9496 Z= 0.297 Angle : 0.639 6.508 12832 Z= 0.342 Chirality : 0.047 0.171 1416 Planarity : 0.005 0.039 1632 Dihedral : 5.152 25.819 1236 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.61 % Allowed : 13.71 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1132 helix: 2.63 (0.29), residues: 260 sheet: 0.64 (0.26), residues: 396 loop : -2.15 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 85 TYR 0.007 0.001 TYR D 225 PHE 0.019 0.002 PHE D 90 TRP 0.007 0.001 TRP A 117 HIS 0.011 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.30 ( 9496) covalent geometry : angle 0.63933 / 0.34 (12832) hydrogen bonds : bond 0.05028 / 3.47 ( 347) hydrogen bonds : angle 5.47216 / 4.06 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.368 Fit side-chains REVERT: A 69 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8488 (t70) REVERT: A 159 ASP cc_start: 0.8869 (t0) cc_final: 0.8549 (t0) REVERT: A 253 GLU cc_start: 0.9118 (tp30) cc_final: 0.8434 (tp30) REVERT: B 69 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8469 (t70) REVERT: B 253 GLU cc_start: 0.9119 (tp30) cc_final: 0.8445 (tp30) REVERT: C 253 GLU cc_start: 0.9135 (tp30) cc_final: 0.8434 (tp30) REVERT: D 159 ASP cc_start: 0.8855 (t0) cc_final: 0.8523 (t0) REVERT: D 253 GLU cc_start: 0.9108 (tp30) cc_final: 0.8399 (tp30) REVERT: D 296 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8948 (ttpp) outliers start: 27 outliers final: 15 residues processed: 106 average time/residue: 0.4517 time to fit residues: 51.8440 Evaluate side-chains 93 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 296 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN B 123 ASN B 286 ASN C 123 ASN C 286 ASN D 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060456 restraints weight = 19108.261| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.72 r_work: 0.2671 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9496 Z= 0.180 Angle : 0.542 5.809 12832 Z= 0.292 Chirality : 0.044 0.149 1416 Planarity : 0.004 0.036 1632 Dihedral : 4.971 24.406 1236 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.41 % Allowed : 15.35 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1132 helix: 2.86 (0.30), residues: 264 sheet: 0.62 (0.27), residues: 396 loop : -2.14 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 85 TYR 0.006 0.001 TYR B 57 PHE 0.011 0.002 PHE D 170 TRP 0.005 0.001 TRP A 117 HIS 0.006 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 9496) covalent geometry : angle 0.54167 / 0.29 (12832) hydrogen bonds : bond 0.04259 / 2.93 ( 347) hydrogen bonds : angle 5.20988 / 3.88 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.368 Fit side-chains REVERT: A 69 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (t70) REVERT: A 159 ASP cc_start: 0.8825 (t0) cc_final: 0.8505 (t0) REVERT: A 180 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9039 (p) REVERT: A 253 GLU cc_start: 0.9138 (tp30) cc_final: 0.8403 (tp30) REVERT: B 69 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (t70) REVERT: B 159 ASP cc_start: 0.8889 (t0) cc_final: 0.8579 (t0) REVERT: B 180 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9089 (p) REVERT: B 253 GLU cc_start: 0.9112 (tp30) cc_final: 0.8394 (tp30) REVERT: C 69 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8395 (t70) REVERT: C 159 ASP cc_start: 0.8791 (t0) cc_final: 0.8435 (t0) REVERT: C 180 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9221 (p) REVERT: C 253 GLU cc_start: 0.9134 (tp30) cc_final: 0.8429 (tp30) REVERT: D 69 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (t70) REVERT: D 180 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9117 (p) REVERT: D 253 GLU cc_start: 0.9113 (tp30) cc_final: 0.8395 (tp30) outliers start: 25 outliers final: 7 residues processed: 101 average time/residue: 0.4707 time to fit residues: 51.6793 Evaluate side-chains 90 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 248 GLN C 242 GLN C 248 GLN D 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.079123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.060839 restraints weight = 19365.780| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.74 r_work: 0.2680 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9496 Z= 0.149 Angle : 0.503 5.928 12832 Z= 0.273 Chirality : 0.044 0.144 1416 Planarity : 0.004 0.031 1632 Dihedral : 4.831 23.520 1236 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.22 % Allowed : 16.22 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1132 helix: 3.10 (0.30), residues: 264 sheet: 0.62 (0.27), residues: 396 loop : -2.01 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 85 TYR 0.007 0.001 TYR B 57 PHE 0.011 0.001 PHE A 90 TRP 0.004 0.001 TRP D 117 HIS 0.005 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9496) covalent geometry : angle 0.50315 / 0.27 (12832) hydrogen bonds : bond 0.03906 / 2.68 ( 347) hydrogen bonds : angle 5.06805 / 3.78 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.259 Fit side-chains REVERT: A 69 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8457 (t70) REVERT: A 180 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9070 (p) REVERT: A 253 GLU cc_start: 0.9147 (tp30) cc_final: 0.8414 (tp30) REVERT: B 69 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8452 (t70) REVERT: B 180 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9051 (p) REVERT: B 253 GLU cc_start: 0.9126 (tp30) cc_final: 0.8377 (tp30) REVERT: C 69 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8383 (t70) REVERT: C 180 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9184 (p) REVERT: C 253 GLU cc_start: 0.9126 (tp30) cc_final: 0.8400 (tp30) REVERT: D 69 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8443 (t70) REVERT: D 146 MET cc_start: 0.9311 (mtp) cc_final: 0.9102 (mmt) REVERT: D 180 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9129 (p) REVERT: D 253 GLU cc_start: 0.9085 (tp30) cc_final: 0.8317 (tp30) outliers start: 23 outliers final: 12 residues processed: 104 average time/residue: 0.4144 time to fit residues: 46.9658 Evaluate side-chains 99 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 ASN C 286 ASN D 73 ASN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.058214 restraints weight = 19887.362| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.77 r_work: 0.2620 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9496 Z= 0.261 Angle : 0.574 6.353 12832 Z= 0.311 Chirality : 0.046 0.165 1416 Planarity : 0.004 0.031 1632 Dihedral : 5.098 26.195 1236 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.28 % Allowed : 15.93 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1132 helix: 2.91 (0.30), residues: 260 sheet: 0.47 (0.27), residues: 396 loop : -2.01 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.005 0.001 TYR B 225 PHE 0.016 0.002 PHE B 178 TRP 0.006 0.001 TRP D 117 HIS 0.006 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 ( 9496) covalent geometry : angle 0.57371 / 0.31 (12832) hydrogen bonds : bond 0.04861 / 3.33 ( 347) hydrogen bonds : angle 5.24665 / 3.89 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.394 Fit side-chains REVERT: A 69 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8532 (t70) REVERT: A 180 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9076 (p) REVERT: A 253 GLU cc_start: 0.9191 (tp30) cc_final: 0.8510 (tp30) REVERT: B 180 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9018 (p) REVERT: B 253 GLU cc_start: 0.9186 (tp30) cc_final: 0.8458 (tp30) REVERT: C 180 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9115 (p) REVERT: C 253 GLU cc_start: 0.9203 (tp30) cc_final: 0.8483 (tp30) REVERT: D 146 MET cc_start: 0.9308 (mtp) cc_final: 0.9084 (mmt) REVERT: D 180 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9101 (p) REVERT: D 253 GLU cc_start: 0.9176 (tp30) cc_final: 0.8469 (tp30) REVERT: D 295 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8990 (t) outliers start: 34 outliers final: 16 residues processed: 104 average time/residue: 0.4633 time to fit residues: 52.3863 Evaluate side-chains 103 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061094 restraints weight = 19474.375| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.82 r_work: 0.2687 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9496 Z= 0.115 Angle : 0.487 5.764 12832 Z= 0.265 Chirality : 0.044 0.143 1416 Planarity : 0.003 0.029 1632 Dihedral : 4.806 22.976 1236 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.51 % Allowed : 17.18 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1132 helix: 3.33 (0.30), residues: 260 sheet: 0.61 (0.27), residues: 396 loop : -1.97 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.008 0.001 TYR B 57 PHE 0.011 0.001 PHE A 178 TRP 0.004 0.001 TRP D 117 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 9496) covalent geometry : angle 0.48715 / 0.27 (12832) hydrogen bonds : bond 0.03681 / 2.52 ( 347) hydrogen bonds : angle 5.02382 / 3.76 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.232 Fit side-chains REVERT: A 69 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8442 (t70) REVERT: A 180 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9001 (p) REVERT: A 253 GLU cc_start: 0.9162 (tp30) cc_final: 0.8452 (tp30) REVERT: A 295 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 69 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8444 (t70) REVERT: B 180 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 253 GLU cc_start: 0.9129 (tp30) cc_final: 0.8360 (tp30) REVERT: C 61 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8310 (p0) REVERT: C 69 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8400 (t70) REVERT: C 146 MET cc_start: 0.9131 (mtm) cc_final: 0.8867 (mmm) REVERT: C 180 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9109 (p) REVERT: C 253 GLU cc_start: 0.9191 (tp30) cc_final: 0.8510 (tp30) REVERT: C 272 MET cc_start: 0.8264 (mmm) cc_final: 0.7818 (mmt) REVERT: D 69 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8443 (t70) REVERT: D 146 MET cc_start: 0.9255 (mtp) cc_final: 0.9032 (mmt) REVERT: D 180 THR cc_start: 0.9427 (OUTLIER) cc_final: 0.9035 (p) REVERT: D 253 GLU cc_start: 0.9153 (tp30) cc_final: 0.8452 (tp30) outliers start: 26 outliers final: 11 residues processed: 102 average time/residue: 0.3593 time to fit residues: 40.0488 Evaluate side-chains 97 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN B 73 ASN B 242 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.078637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060121 restraints weight = 19602.493| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.78 r_work: 0.2661 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9496 Z= 0.169 Angle : 0.504 6.078 12832 Z= 0.275 Chirality : 0.044 0.151 1416 Planarity : 0.003 0.030 1632 Dihedral : 4.811 23.603 1236 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.70 % Allowed : 16.99 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1132 helix: 3.22 (0.30), residues: 260 sheet: 0.59 (0.27), residues: 396 loop : -1.99 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.006 0.001 TYR C 57 PHE 0.012 0.002 PHE B 178 TRP 0.005 0.001 TRP B 117 HIS 0.005 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 9496) covalent geometry : angle 0.50400 / 0.27 (12832) hydrogen bonds : bond 0.04047 / 2.77 ( 347) hydrogen bonds : angle 5.03256 / 3.76 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.263 Fit side-chains REVERT: A 61 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8330 (p0) REVERT: A 69 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8505 (t70) REVERT: A 180 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.8978 (p) REVERT: A 253 GLU cc_start: 0.9191 (tp30) cc_final: 0.8444 (tp30) REVERT: B 69 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8496 (t70) REVERT: B 180 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9047 (p) REVERT: B 253 GLU cc_start: 0.9159 (tp30) cc_final: 0.8422 (tp30) REVERT: C 61 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8346 (p0) REVERT: C 69 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8484 (t70) REVERT: C 180 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9110 (p) REVERT: C 253 GLU cc_start: 0.9199 (tp30) cc_final: 0.8459 (tp30) REVERT: C 272 MET cc_start: 0.8114 (mmm) cc_final: 0.7895 (mmt) REVERT: D 36 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8781 (ptmm) REVERT: D 69 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8495 (t70) REVERT: D 146 MET cc_start: 0.9286 (mtp) cc_final: 0.9040 (mmt) REVERT: D 180 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9045 (p) REVERT: D 253 GLU cc_start: 0.9167 (tp30) cc_final: 0.8413 (tp30) REVERT: D 295 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8925 (t) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 0.3985 time to fit residues: 47.9058 Evaluate side-chains 96 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN B 73 ASN B 123 ASN C 73 ASN C 123 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 123 ASN D 248 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.061499 restraints weight = 19273.574| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.79 r_work: 0.2692 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9496 Z= 0.124 Angle : 0.488 5.870 12832 Z= 0.266 Chirality : 0.044 0.138 1416 Planarity : 0.003 0.029 1632 Dihedral : 4.674 21.848 1236 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.90 % Allowed : 17.76 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1132 helix: 3.35 (0.31), residues: 260 sheet: 0.64 (0.27), residues: 396 loop : -1.92 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 202 TYR 0.007 0.001 TYR B 57 PHE 0.012 0.001 PHE B 178 TRP 0.004 0.001 TRP B 117 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 9496) covalent geometry : angle 0.48813 / 0.27 (12832) hydrogen bonds : bond 0.03575 / 2.44 ( 347) hydrogen bonds : angle 4.93966 / 3.71 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.381 Fit side-chains REVERT: A 36 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8794 (ptmm) REVERT: A 61 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8338 (p0) REVERT: A 69 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8464 (t70) REVERT: A 146 MET cc_start: 0.9132 (mtm) cc_final: 0.8786 (mmm) REVERT: A 180 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.8972 (p) REVERT: A 253 GLU cc_start: 0.9156 (tp30) cc_final: 0.8344 (tp30) REVERT: B 61 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8374 (p0) REVERT: B 69 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8471 (t70) REVERT: B 180 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9047 (p) REVERT: B 253 GLU cc_start: 0.9149 (tp30) cc_final: 0.8338 (tp30) REVERT: C 61 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8361 (p0) REVERT: C 69 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8446 (t70) REVERT: C 146 MET cc_start: 0.9149 (mtm) cc_final: 0.8807 (mmm) REVERT: C 180 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.9054 (p) REVERT: C 253 GLU cc_start: 0.9193 (tp30) cc_final: 0.8440 (tp30) REVERT: C 294 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8084 (t) REVERT: D 69 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8455 (t70) REVERT: D 146 MET cc_start: 0.9278 (mtp) cc_final: 0.9022 (mmt) REVERT: D 180 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9027 (p) REVERT: D 253 GLU cc_start: 0.9167 (tp30) cc_final: 0.8421 (tp30) outliers start: 30 outliers final: 10 residues processed: 115 average time/residue: 0.4660 time to fit residues: 58.1133 Evaluate side-chains 98 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN B 123 ASN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 123 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 123 ASN D 286 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.077600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.059111 restraints weight = 19559.041| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.77 r_work: 0.2640 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9496 Z= 0.240 Angle : 0.562 7.214 12832 Z= 0.302 Chirality : 0.045 0.161 1416 Planarity : 0.004 0.032 1632 Dihedral : 4.877 24.238 1236 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.80 % Allowed : 18.63 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1132 helix: 3.09 (0.30), residues: 260 sheet: 0.57 (0.27), residues: 396 loop : -2.00 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 202 TYR 0.006 0.001 TYR B 37 PHE 0.026 0.002 PHE A 178 TRP 0.006 0.001 TRP A 117 HIS 0.006 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 ( 9496) covalent geometry : angle 0.56183 / 0.30 (12832) hydrogen bonds : bond 0.04462 / 3.05 ( 347) hydrogen bonds : angle 5.10585 / 3.81 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.238 Fit side-chains REVERT: A 61 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8361 (p0) REVERT: A 69 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (t70) REVERT: A 180 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9024 (p) REVERT: A 253 GLU cc_start: 0.9211 (tp30) cc_final: 0.8382 (tp30) REVERT: A 272 MET cc_start: 0.8383 (mmm) cc_final: 0.8153 (mmt) REVERT: B 61 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8384 (p0) REVERT: B 69 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8542 (t70) REVERT: B 180 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9037 (p) REVERT: B 253 GLU cc_start: 0.9177 (tp30) cc_final: 0.8378 (tp30) REVERT: C 61 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8387 (p0) REVERT: C 69 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (t70) REVERT: C 180 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9134 (p) REVERT: C 253 GLU cc_start: 0.9221 (tp30) cc_final: 0.8506 (tp30) REVERT: D 69 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8532 (t70) REVERT: D 146 MET cc_start: 0.9280 (mtp) cc_final: 0.9021 (mmt) REVERT: D 180 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9101 (p) REVERT: D 253 GLU cc_start: 0.9190 (tp30) cc_final: 0.8450 (tp30) outliers start: 29 outliers final: 14 residues processed: 105 average time/residue: 0.4029 time to fit residues: 46.1146 Evaluate side-chains 100 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 73 ASN B 123 ASN C 73 ASN C 123 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.060279 restraints weight = 19409.647| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.77 r_work: 0.2666 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9496 Z= 0.174 Angle : 0.535 7.113 12832 Z= 0.288 Chirality : 0.044 0.148 1416 Planarity : 0.004 0.031 1632 Dihedral : 4.845 23.312 1236 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.80 % Allowed : 19.11 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1132 helix: 3.15 (0.30), residues: 260 sheet: 0.64 (0.27), residues: 396 loop : -1.94 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 202 TYR 0.006 0.001 TYR C 57 PHE 0.016 0.002 PHE A 178 TRP 0.005 0.001 TRP D 117 HIS 0.005 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 9496) covalent geometry : angle 0.53468 / 0.29 (12832) hydrogen bonds : bond 0.04020 / 2.74 ( 347) hydrogen bonds : angle 5.04786 / 3.79 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.322 Fit side-chains REVERT: A 61 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8367 (p0) REVERT: A 69 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8488 (t70) REVERT: A 180 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 253 GLU cc_start: 0.9211 (tp30) cc_final: 0.8363 (tp30) REVERT: B 61 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8384 (p0) REVERT: B 69 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8512 (t70) REVERT: B 180 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9096 (p) REVERT: B 253 GLU cc_start: 0.9187 (tp30) cc_final: 0.8417 (tp30) REVERT: C 61 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8387 (p0) REVERT: C 69 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8496 (t70) REVERT: C 146 MET cc_start: 0.9145 (mtm) cc_final: 0.8800 (mmm) REVERT: C 180 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9091 (p) REVERT: C 253 GLU cc_start: 0.9212 (tp30) cc_final: 0.8512 (tp30) REVERT: D 69 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8485 (t70) REVERT: D 146 MET cc_start: 0.9271 (mtp) cc_final: 0.9014 (mmt) REVERT: D 180 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9088 (p) REVERT: D 253 GLU cc_start: 0.9178 (tp30) cc_final: 0.8440 (tp30) outliers start: 29 outliers final: 14 residues processed: 105 average time/residue: 0.4065 time to fit residues: 46.4711 Evaluate side-chains 106 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 100 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 ASN B 73 ASN B 123 ASN C 73 ASN C 123 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.060093 restraints weight = 19345.836| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.76 r_work: 0.2665 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9496 Z= 0.181 Angle : 0.542 8.269 12832 Z= 0.289 Chirality : 0.044 0.150 1416 Planarity : 0.004 0.032 1632 Dihedral : 4.843 23.528 1236 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.70 % Allowed : 19.02 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1132 helix: 3.13 (0.30), residues: 260 sheet: 0.61 (0.27), residues: 396 loop : -1.93 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 202 TYR 0.006 0.001 TYR B 57 PHE 0.017 0.002 PHE C 178 TRP 0.005 0.001 TRP D 117 HIS 0.005 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 9496) covalent geometry : angle 0.54188 / 0.29 (12832) hydrogen bonds : bond 0.04092 / 2.80 ( 347) hydrogen bonds : angle 5.06145 / 3.79 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.37 seconds wall clock time: 37 minutes 27.08 seconds (2247.08 seconds total)