Starting phenix.real_space_refine on Wed Aug 5 10:18:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bog_44735/08_2026/9bog_44735.map" } resolution = 3.99 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= 0.001 sd= 0.026 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 20 5.16 5 C 5838 2.51 5 N 1705 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 9370 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 5496 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 31, 'TRANS': 768} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 913 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'ASP:plan': 24, 'ARG:plan': 15, 'GLU:plan': 16, 'GLN:plan1': 16, 'TYR:plan': 8, 'ASN:plan1': 18, 'PHE:plan': 2, 'HIS:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 439 Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 154, 884 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 145} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 12, 'PHE:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 6, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1356 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 14, 'TRANS': 190} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 7, 'ASN:plan1': 8, 'GLN:plan1': 2, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1634 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 262} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'PHE:plan': 6, 'ASN:plan1': 15, 'TYR:plan': 10, 'GLN:plan1': 7, 'HIS:plan': 1, 'ASP:plan': 7, 'GLU:plan': 2, 'ARG:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 251 Time building chain proxies: 2.26, per 1000 atoms: 0.24 Number of scatterers: 9370 At special positions: 0 Unit cell: (81.6, 92.4, 163.2, 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 20 16.00 O 1807 8.00 N 1705 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 832 " distance=2.04 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 56 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 187 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 375.1 milliseconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 25 sheets defined 5.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 removed outlier: 4.200A pdb=" N LEU D 9 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 4.177A pdb=" N ASN D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.752A pdb=" N ARG D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 448 removed outlier: 3.563A pdb=" N THR D 447 " --> pdb=" O ASN D 443 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR D 448 " --> pdb=" O PHE D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 443 through 448' Processing helix chain 'D' and resid 817 through 822 removed outlier: 3.655A pdb=" N GLN D 821 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 36 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.188A pdb=" N ALA C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 69 Processing sheet with id=AA1, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.002A pdb=" N TYR D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU D 39 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 45 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP D 36 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 113 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR D 38 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 152 through 153 current: chain 'D' and resid 161 through 170 removed outlier: 4.308A pdb=" N ASN D 202 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 182 " --> pdb=" O HIS D 200 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS D 200 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER D 184 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP D 198 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 15.876A pdb=" N ILE D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N TYR D 222 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR D 203 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR D 331 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 376 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE D 429 " --> pdb=" O THR D 489 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR D 489 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 431 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ARG D 481 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY D 482 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 647 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 256 through 260 Processing sheet with id=AA5, first strand: chain 'D' and resid 273 through 280 removed outlier: 6.877A pdb=" N ILE D 268 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 266 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D 279 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA D 264 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 700 through 701 Processing sheet with id=AA7, first strand: chain 'D' and resid 711 through 714 Processing sheet with id=AA8, first strand: chain 'D' and resid 725 through 726 Processing sheet with id=AA9, first strand: chain 'D' and resid 762 through 763 removed outlier: 6.935A pdb=" N LEU D 753 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER D 790 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET D 755 " --> pdb=" O TYR D 788 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR D 788 " --> pdb=" O MET D 755 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 757 " --> pdb=" O GLN D 786 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN D 786 " --> pdb=" O LEU D 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 762 through 763 Processing sheet with id=AB2, first strand: chain 'D' and resid 778 through 780 Processing sheet with id=AB3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.541A pdb=" N VAL H 170 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER F 3 " --> pdb=" O VAL H 274 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 9 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN H 191 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA H 242 " --> pdb=" O GLN H 191 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU H 193 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.561A pdb=" N ALA F 19 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 52 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 23 through 24 removed outlier: 7.305A pdb=" N VAL C 9 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ARG C 116 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR C 11 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 116 removed outlier: 4.075A pdb=" N ALA F 145 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 104 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA F 147 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE F 149 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 108 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 110 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'C' and resid 132 through 135 Processing sheet with id=AB9, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 152 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 165 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.626A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 152 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 190 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C 154 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG C 188 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 187 " --> pdb=" O MET C 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AC3, first strand: chain 'H' and resid 16 through 22 removed outlier: 6.459A pdb=" N PHE H 142 " --> pdb=" O ARG H 132 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG H 132 " --> pdb=" O PHE H 142 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE H 144 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 130 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 146 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL H 128 " --> pdb=" O TRP H 146 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE H 148 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE H 126 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA H 63 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL H 128 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY H 61 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE H 130 " --> pdb=" O GLN H 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 34 through 37 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 120 removed outlier: 3.786A pdb=" N GLY H 117 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL H 154 " --> pdb=" O ALA H 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.517A pdb=" N LEU H 252 " --> pdb=" O ILE H 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 184 through 185 422 hydrogen bonds defined for protein. 1083 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: 1.77 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3285 1.34 - 1.46: 2211 1.46 - 1.58: 3996 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 9522 Sorted by residual: bond pdb=" CB ASP C 78 " pdb=" CG ASP C 78 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CB TRP D 183 " pdb=" CG TRP D 183 " ideal model delta sigma weight residual 1.498 1.527 -0.029 3.10e-02 1.04e+03 8.47e-01 bond pdb=" CB ASP C 192 " pdb=" CG ASP C 192 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.23e-01 bond pdb=" CA VAL D 16 " pdb=" CB VAL D 16 " ideal model delta sigma weight residual 1.548 1.538 0.010 1.13e-02 7.83e+03 7.24e-01 ... (remaining 9517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12886 1.79 - 3.57: 161 3.57 - 5.36: 25 5.36 - 7.14: 3 7.14 - 8.93: 4 Bond angle restraints: 13079 Sorted by residual: angle pdb=" N ILE D 275 " pdb=" CA ILE D 275 " pdb=" C ILE D 275 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CB MET C 57 " pdb=" CG MET C 57 " pdb=" SD MET C 57 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" CA CYS D 810 " pdb=" CB CYS D 810 " pdb=" SG CYS D 810 " ideal model delta sigma weight residual 114.40 120.34 -5.94 2.30e+00 1.89e-01 6.67e+00 angle pdb=" CA LEU D 582 " pdb=" CB LEU D 582 " pdb=" CG LEU D 582 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" CA LEU H 172 " pdb=" CB LEU H 172 " pdb=" CG LEU H 172 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.56e+00 ... (remaining 13074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4950 17.91 - 35.82: 463 35.82 - 53.73: 97 53.73 - 71.64: 14 71.64 - 89.55: 4 Dihedral angle restraints: 5528 sinusoidal: 1431 harmonic: 4097 Sorted by residual: dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 90 " pdb=" CB CYS D 90 " ideal model delta sinusoidal sigma weight residual 93.00 163.99 -70.99 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS H 161 " pdb=" SG CYS H 161 " pdb=" SG CYS H 187 " pdb=" CB CYS H 187 " ideal model delta sinusoidal sigma weight residual 93.00 52.93 40.07 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE D 525 " pdb=" C PHE D 525 " pdb=" N GLU D 526 " pdb=" CA GLU D 526 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 948 0.030 - 0.059: 395 0.059 - 0.089: 98 0.089 - 0.119: 112 0.119 - 0.148: 16 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA VAL D 320 " pdb=" N VAL D 320 " pdb=" C VAL D 320 " pdb=" CB VAL D 320 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CG LEU H 172 " pdb=" CB LEU H 172 " pdb=" CD1 LEU H 172 " pdb=" CD2 LEU H 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE D 259 " pdb=" N ILE D 259 " pdb=" C ILE D 259 " pdb=" CB ILE D 259 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1566 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 320 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO D 321 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 52 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO C 53 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 167 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" CG ASP H 167 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP H 167 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 918 2.75 - 3.29: 8369 3.29 - 3.83: 14033 3.83 - 4.36: 14405 4.36 - 4.90: 27039 Nonbonded interactions: 64764 Sorted by model distance: nonbonded pdb=" O THR C 189 " pdb=" OG1 THR C 197 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR H 226 " pdb=" OG1 THR H 253 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR D 375 " pdb=" O PHE D 442 " model vdw 2.245 3.040 nonbonded pdb=" O SER H 216 " pdb=" OG SER H 216 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASN C 39 " pdb=" N ALA C 40 " model vdw 2.309 3.120 ... (remaining 64759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.530 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.002 0.036 9527 Z= 0.098 Angle : 0.537 8.927 13089 Z= 0.286 Chirality : 0.043 0.148 1569 Planarity : 0.003 0.060 1758 Dihedral : 14.608 89.553 2897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.29 % Allowed : 32.65 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.22), residues: 1424 helix: -1.56 (0.77), residues: 49 sheet: 0.83 (0.21), residues: 625 loop : -0.40 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 8 TYR 0.014 0.001 TYR D 593 PHE 0.008 0.001 PHE D 525 TRP 0.009 0.001 TRP D 508 HIS 0.007 0.001 HIS D 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 9522) covalent geometry : angle 0.53628 / 0.29 (13079) SS BOND : bond 0.00427 / 0.23 ( 5) SS BOND : angle 1.08155 / 0.41 ( 10) hydrogen bonds : bond 0.14610 / 10.93 ( 419) hydrogen bonds : angle 6.25196 / 4.85 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 257 HIS cc_start: 0.6898 (m-70) cc_final: 0.6329 (m90) REVERT: D 324 GLN cc_start: 0.5958 (mm-40) cc_final: 0.5685 (mm110) REVERT: D 332 SER cc_start: 0.7158 (t) cc_final: 0.6880 (p) REVERT: D 379 ASN cc_start: 0.7298 (t0) cc_final: 0.7097 (m-40) REVERT: D 400 ASN cc_start: 0.8167 (m-40) cc_final: 0.7937 (t0) REVERT: D 416 PHE cc_start: 0.6806 (m-80) cc_final: 0.6591 (m-80) REVERT: D 484 LEU cc_start: 0.8478 (tp) cc_final: 0.8277 (tp) REVERT: D 518 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 531 THR cc_start: 0.7266 (t) cc_final: 0.6973 (p) REVERT: D 537 THR cc_start: 0.7912 (m) cc_final: 0.7663 (p) REVERT: D 553 VAL cc_start: 0.8645 (t) cc_final: 0.8438 (m) REVERT: D 599 ASP cc_start: 0.7532 (t0) cc_final: 0.6966 (t0) REVERT: D 608 THR cc_start: 0.7986 (t) cc_final: 0.7493 (p) REVERT: D 636 ASN cc_start: 0.7805 (p0) cc_final: 0.7546 (p0) REVERT: D 669 LEU cc_start: 0.8051 (mp) cc_final: 0.7794 (mt) REVERT: D 688 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (m110) REVERT: D 756 THR cc_start: 0.8757 (m) cc_final: 0.8533 (p) REVERT: D 786 GLN cc_start: 0.7250 (mt0) cc_final: 0.6992 (mt0) REVERT: D 829 SER cc_start: 0.8534 (t) cc_final: 0.8168 (p) REVERT: F 4 THR cc_start: 0.8555 (m) cc_final: 0.8202 (p) REVERT: F 123 ASN cc_start: 0.7878 (t0) cc_final: 0.7514 (t0) REVERT: C 4 LEU cc_start: 0.8468 (mt) cc_final: 0.8191 (mp) REVERT: C 19 GLN cc_start: 0.7992 (mt0) cc_final: 0.7730 (mt0) REVERT: C 22 VAL cc_start: 0.8537 (t) cc_final: 0.8194 (p) REVERT: C 44 LYS cc_start: 0.9198 (tppp) cc_final: 0.8961 (mttm) REVERT: H 191 GLN cc_start: 0.8074 (pt0) cc_final: 0.7866 (pt0) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.0879 time to fit residues: 38.3561 Evaluate side-chains 284 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 688 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 711 ASN D 809 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107175 restraints weight = 17359.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110407 restraints weight = 9673.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112507 restraints weight = 6209.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114036 restraints weight = 4452.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114965 restraints weight = 3458.777| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9527 Z= 0.150 Angle : 0.581 9.732 13089 Z= 0.299 Chirality : 0.045 0.159 1569 Planarity : 0.004 0.060 1758 Dihedral : 3.433 16.403 1521 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 8.02 % Allowed : 29.01 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.23), residues: 1424 helix: -1.78 (0.78), residues: 44 sheet: 0.85 (0.20), residues: 640 loop : -0.29 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 258 TYR 0.017 0.002 TYR D 650 PHE 0.011 0.001 PHE D 4 TRP 0.013 0.002 TRP D 183 HIS 0.005 0.001 HIS D 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9522) covalent geometry : angle 0.58059 / 0.30 (13079) SS BOND : bond 0.00334 / 0.18 ( 5) SS BOND : angle 0.86890 / 0.39 ( 10) hydrogen bonds : bond 0.03389 / 2.49 ( 419) hydrogen bonds : angle 5.21839 / 3.95 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: D 237 GLN cc_start: 0.7977 (tt0) cc_final: 0.7775 (tt0) REVERT: D 240 SER cc_start: 0.8486 (m) cc_final: 0.8268 (m) REVERT: D 257 HIS cc_start: 0.7223 (m-70) cc_final: 0.6933 (m90) REVERT: D 324 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6381 (mm-40) REVERT: D 332 SER cc_start: 0.7759 (t) cc_final: 0.7453 (p) REVERT: D 346 GLU cc_start: 0.7131 (mp0) cc_final: 0.6914 (mp0) REVERT: D 379 ASN cc_start: 0.7903 (t0) cc_final: 0.7500 (t0) REVERT: D 394 VAL cc_start: 0.8275 (p) cc_final: 0.7937 (m) REVERT: D 489 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7864 (p) REVERT: D 518 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 531 THR cc_start: 0.7463 (t) cc_final: 0.7134 (p) REVERT: D 537 THR cc_start: 0.7982 (m) cc_final: 0.7647 (p) REVERT: D 599 ASP cc_start: 0.7880 (t70) cc_final: 0.7577 (t0) REVERT: D 608 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (p) REVERT: D 636 ASN cc_start: 0.8008 (p0) cc_final: 0.7806 (p0) REVERT: D 647 GLN cc_start: 0.7445 (pt0) cc_final: 0.7073 (pt0) REVERT: D 669 LEU cc_start: 0.8496 (mp) cc_final: 0.8236 (mt) REVERT: D 683 ASP cc_start: 0.7699 (t0) cc_final: 0.7399 (t0) REVERT: D 688 ASN cc_start: 0.7885 (m110) cc_final: 0.7656 (m110) REVERT: D 706 THR cc_start: 0.8054 (p) cc_final: 0.7769 (t) REVERT: D 741 VAL cc_start: 0.8060 (t) cc_final: 0.7721 (p) REVERT: D 786 GLN cc_start: 0.7361 (mt0) cc_final: 0.7051 (mt0) REVERT: F 4 THR cc_start: 0.8583 (m) cc_final: 0.8204 (p) REVERT: F 123 ASN cc_start: 0.7936 (t0) cc_final: 0.7448 (t0) REVERT: C 4 LEU cc_start: 0.8543 (mt) cc_final: 0.8310 (mp) REVERT: C 75 LEU cc_start: 0.8204 (mm) cc_final: 0.7909 (mt) REVERT: C 151 THR cc_start: 0.8680 (m) cc_final: 0.8304 (p) REVERT: H 37 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6581 (t0) REVERT: H 167 ASP cc_start: 0.7302 (t0) cc_final: 0.7014 (t0) REVERT: H 186 TYR cc_start: 0.7620 (p90) cc_final: 0.7362 (p90) REVERT: H 191 GLN cc_start: 0.8885 (pt0) cc_final: 0.8505 (pt0) REVERT: H 269 GLN cc_start: 0.8213 (tt0) cc_final: 0.7424 (tt0) REVERT: H 271 ILE cc_start: 0.8681 (mm) cc_final: 0.8364 (mm) outliers start: 55 outliers final: 27 residues processed: 315 average time/residue: 0.0750 time to fit residues: 34.3667 Evaluate side-chains 305 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 239 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 588 ASN D 711 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102012 restraints weight = 17449.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105267 restraints weight = 9893.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107467 restraints weight = 6472.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108950 restraints weight = 4696.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109884 restraints weight = 3722.935| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9527 Z= 0.183 Angle : 0.596 13.306 13089 Z= 0.309 Chirality : 0.046 0.187 1569 Planarity : 0.004 0.062 1758 Dihedral : 3.689 16.859 1519 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 7.87 % Allowed : 31.78 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.10 (0.23), residues: 1424 helix: -1.76 (0.75), residues: 44 sheet: 0.78 (0.20), residues: 646 loop : -0.43 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 709 TYR 0.018 0.002 TYR D 338 PHE 0.027 0.002 PHE C 55 TRP 0.015 0.002 TRP D 204 HIS 0.010 0.002 HIS D 809 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 9522) covalent geometry : angle 0.59563 / 0.31 (13079) SS BOND : bond 0.00292 / 0.16 ( 5) SS BOND : angle 0.75716 / 0.35 ( 10) hydrogen bonds : bond 0.03599 / 2.64 ( 419) hydrogen bonds : angle 5.23189 / 3.93 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: D 324 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6421 (mm110) REVERT: D 328 HIS cc_start: 0.8072 (t-90) cc_final: 0.7853 (t-90) REVERT: D 379 ASN cc_start: 0.7944 (t0) cc_final: 0.7570 (t0) REVERT: D 386 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6826 (mtp) REVERT: D 416 PHE cc_start: 0.7306 (m-80) cc_final: 0.7093 (m-10) REVERT: D 484 LEU cc_start: 0.8534 (tp) cc_final: 0.8316 (tt) REVERT: D 489 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (p) REVERT: D 518 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 537 THR cc_start: 0.7929 (m) cc_final: 0.7587 (p) REVERT: D 557 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: D 588 ASN cc_start: 0.8405 (m-40) cc_final: 0.8169 (m-40) REVERT: D 599 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7702 (t0) REVERT: D 608 THR cc_start: 0.7920 (t) cc_final: 0.7420 (p) REVERT: D 647 GLN cc_start: 0.7488 (pt0) cc_final: 0.7110 (pt0) REVERT: D 669 LEU cc_start: 0.8517 (mp) cc_final: 0.8298 (mt) REVERT: D 683 ASP cc_start: 0.7735 (t0) cc_final: 0.7378 (t0) REVERT: D 688 ASN cc_start: 0.7925 (m110) cc_final: 0.7666 (m110) REVERT: D 706 THR cc_start: 0.8140 (p) cc_final: 0.7939 (t) REVERT: D 728 ASN cc_start: 0.7663 (t0) cc_final: 0.7422 (t0) REVERT: D 741 VAL cc_start: 0.8132 (t) cc_final: 0.7891 (p) REVERT: D 786 GLN cc_start: 0.7349 (mt0) cc_final: 0.7099 (mt0) REVERT: F 4 THR cc_start: 0.8628 (m) cc_final: 0.8265 (p) REVERT: F 64 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8098 (mttm) REVERT: F 65 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8711 (p) REVERT: F 123 ASN cc_start: 0.7963 (t0) cc_final: 0.7416 (t0) REVERT: C 55 PHE cc_start: 0.8205 (p90) cc_final: 0.7955 (p90) REVERT: C 75 LEU cc_start: 0.8268 (mm) cc_final: 0.7962 (mt) REVERT: C 151 THR cc_start: 0.8663 (m) cc_final: 0.8263 (p) REVERT: H 37 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6640 (t0) REVERT: H 167 ASP cc_start: 0.7343 (t0) cc_final: 0.7012 (t0) REVERT: H 186 TYR cc_start: 0.7617 (p90) cc_final: 0.7360 (p90) REVERT: H 191 GLN cc_start: 0.8921 (pt0) cc_final: 0.8508 (pt0) REVERT: H 269 GLN cc_start: 0.8360 (tt0) cc_final: 0.7962 (tt0) outliers start: 54 outliers final: 33 residues processed: 305 average time/residue: 0.0834 time to fit residues: 36.8310 Evaluate side-chains 318 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 TRP Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 46 optimal weight: 2.9990 chunk 70 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.852 > 50:) chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 3 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 257 HIS D 711 ASN D 809 HIS C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101850 restraints weight = 17430.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105037 restraints weight = 9723.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107150 restraints weight = 6250.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108639 restraints weight = 4478.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109454 restraints weight = 3493.538| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9527 Z= 0.207 Angle : 0.602 9.294 13089 Z= 0.318 Chirality : 0.046 0.192 1569 Planarity : 0.004 0.056 1758 Dihedral : 4.033 18.967 1519 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 8.89 % Allowed : 30.76 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.10 (0.22), residues: 1424 helix: -1.68 (0.77), residues: 44 sheet: 0.69 (0.20), residues: 632 loop : -0.60 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 47 TYR 0.018 0.002 TYR D 366 PHE 0.024 0.002 PHE C 55 TRP 0.017 0.002 TRP D 204 HIS 0.009 0.002 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 9522) covalent geometry : angle 0.60201 / 0.32 (13079) SS BOND : bond 0.00345 / 0.19 ( 5) SS BOND : angle 0.78562 / 0.38 ( 10) hydrogen bonds : bond 0.03626 / 2.67 ( 419) hydrogen bonds : angle 5.41193 / 4.04 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 322 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8126 (pp) REVERT: D 323 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7555 (mm) REVERT: D 344 GLN cc_start: 0.7984 (pm20) cc_final: 0.7685 (pt0) REVERT: D 379 ASN cc_start: 0.7914 (t0) cc_final: 0.7357 (t0) REVERT: D 382 ILE cc_start: 0.8142 (mp) cc_final: 0.7793 (mm) REVERT: D 386 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6816 (mtp) REVERT: D 484 LEU cc_start: 0.8564 (tp) cc_final: 0.8306 (tt) REVERT: D 489 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7999 (p) REVERT: D 503 SER cc_start: 0.8640 (m) cc_final: 0.8173 (p) REVERT: D 518 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 532 LEU cc_start: 0.8687 (tp) cc_final: 0.8392 (tp) REVERT: D 537 THR cc_start: 0.7965 (m) cc_final: 0.7626 (p) REVERT: D 557 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: D 588 ASN cc_start: 0.8358 (m-40) cc_final: 0.8142 (m-40) REVERT: D 599 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (t0) REVERT: D 608 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7410 (p) REVERT: D 634 ASN cc_start: 0.8000 (m110) cc_final: 0.7742 (m110) REVERT: D 647 GLN cc_start: 0.7466 (pt0) cc_final: 0.7156 (pt0) REVERT: D 683 ASP cc_start: 0.7768 (t0) cc_final: 0.7482 (t0) REVERT: D 741 VAL cc_start: 0.8085 (t) cc_final: 0.7866 (p) REVERT: D 745 PHE cc_start: 0.7572 (m-80) cc_final: 0.7307 (m-10) REVERT: D 756 THR cc_start: 0.8771 (m) cc_final: 0.8404 (p) REVERT: D 784 ASN cc_start: 0.8018 (m-40) cc_final: 0.7379 (t0) REVERT: D 786 GLN cc_start: 0.7203 (mt0) cc_final: 0.6872 (mt0) REVERT: F 4 THR cc_start: 0.8557 (m) cc_final: 0.8214 (p) REVERT: F 64 LYS cc_start: 0.8288 (ttmm) cc_final: 0.8061 (mttm) REVERT: F 65 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8720 (p) REVERT: F 123 ASN cc_start: 0.7992 (t0) cc_final: 0.7465 (t0) REVERT: C 55 PHE cc_start: 0.8271 (p90) cc_final: 0.7984 (p90) REVERT: C 75 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (mt) REVERT: C 151 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8289 (p) REVERT: H 37 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6783 (t0) REVERT: H 167 ASP cc_start: 0.7354 (t0) cc_final: 0.7039 (t0) REVERT: H 186 TYR cc_start: 0.7675 (p90) cc_final: 0.7325 (p90) REVERT: H 191 GLN cc_start: 0.8838 (pt0) cc_final: 0.8447 (pt0) outliers start: 61 outliers final: 39 residues processed: 316 average time/residue: 0.0814 time to fit residues: 37.6676 Evaluate side-chains 330 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 27 optimal weight: 0.0770 chunk 17 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 88 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 237 GLN D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107425 restraints weight = 17588.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110787 restraints weight = 9889.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113046 restraints weight = 6395.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114621 restraints weight = 4623.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115638 restraints weight = 3625.178| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9527 Z= 0.122 Angle : 0.588 8.861 13089 Z= 0.302 Chirality : 0.046 0.297 1569 Planarity : 0.004 0.087 1758 Dihedral : 3.808 18.672 1519 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.12 % Allowed : 35.13 % Favored : 58.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.07 (0.22), residues: 1424 helix: -1.55 (0.81), residues: 44 sheet: 0.73 (0.20), residues: 635 loop : -0.63 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 709 TYR 0.013 0.001 TYR D 650 PHE 0.018 0.001 PHE C 55 TRP 0.013 0.001 TRP D 183 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9522) covalent geometry : angle 0.58826 / 0.30 (13079) SS BOND : bond 0.00283 / 0.18 ( 5) SS BOND : angle 0.66578 / 0.31 ( 10) hydrogen bonds : bond 0.03091 / 2.29 ( 419) hydrogen bonds : angle 5.19158 / 3.86 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7841 (m-10) cc_final: 0.7538 (m-10) REVERT: D 259 ILE cc_start: 0.7762 (mm) cc_final: 0.6123 (pt) REVERT: D 295 ASN cc_start: 0.8221 (p0) cc_final: 0.7970 (p0) REVERT: D 323 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7416 (mm) REVERT: D 331 TYR cc_start: 0.7734 (p90) cc_final: 0.7468 (p90) REVERT: D 379 ASN cc_start: 0.8089 (t0) cc_final: 0.7600 (t0) REVERT: D 382 ILE cc_start: 0.8094 (mp) cc_final: 0.7793 (mm) REVERT: D 394 VAL cc_start: 0.8074 (p) cc_final: 0.7772 (m) REVERT: D 489 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8012 (p) REVERT: D 503 SER cc_start: 0.8588 (m) cc_final: 0.8167 (p) REVERT: D 518 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 537 THR cc_start: 0.7981 (m) cc_final: 0.7664 (p) REVERT: D 608 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7472 (p) REVERT: D 634 ASN cc_start: 0.7771 (m110) cc_final: 0.6740 (m110) REVERT: D 647 GLN cc_start: 0.7475 (pt0) cc_final: 0.7140 (pt0) REVERT: D 683 ASP cc_start: 0.7696 (t0) cc_final: 0.7383 (t0) REVERT: D 695 ASP cc_start: 0.6612 (p0) cc_final: 0.6397 (p0) REVERT: D 709 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.7024 (ttp-170) REVERT: D 728 ASN cc_start: 0.7347 (t0) cc_final: 0.7141 (t0) REVERT: D 741 VAL cc_start: 0.8049 (t) cc_final: 0.7836 (p) REVERT: D 746 LYS cc_start: 0.8179 (mmmm) cc_final: 0.7967 (mmmm) REVERT: D 756 THR cc_start: 0.8678 (m) cc_final: 0.8054 (p) REVERT: D 784 ASN cc_start: 0.8002 (m-40) cc_final: 0.7278 (t0) REVERT: D 786 GLN cc_start: 0.7286 (mt0) cc_final: 0.6977 (mt0) REVERT: F 4 THR cc_start: 0.8551 (m) cc_final: 0.8196 (p) REVERT: F 65 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8670 (p) REVERT: F 123 ASN cc_start: 0.7849 (t0) cc_final: 0.7342 (t0) REVERT: C 55 PHE cc_start: 0.8256 (p90) cc_final: 0.8017 (p90) REVERT: C 75 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7915 (mt) REVERT: C 151 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8298 (p) REVERT: H 37 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6794 (t0) REVERT: H 167 ASP cc_start: 0.7287 (t0) cc_final: 0.6992 (t0) REVERT: H 186 TYR cc_start: 0.7621 (p90) cc_final: 0.7274 (p90) REVERT: H 191 GLN cc_start: 0.8789 (pt0) cc_final: 0.8485 (pt0) outliers start: 42 outliers final: 28 residues processed: 311 average time/residue: 0.0829 time to fit residues: 37.6272 Evaluate side-chains 323 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 36 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 237 GLN D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.101988 restraints weight = 17653.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105477 restraints weight = 9779.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107848 restraints weight = 6262.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109442 restraints weight = 4479.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110573 restraints weight = 3484.342| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9527 Z= 0.117 Angle : 0.591 8.475 13089 Z= 0.302 Chirality : 0.045 0.180 1569 Planarity : 0.004 0.073 1758 Dihedral : 3.717 18.569 1519 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.71 % Allowed : 34.55 % Favored : 58.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.04 (0.22), residues: 1424 helix: -1.50 (0.82), residues: 44 sheet: 0.78 (0.20), residues: 634 loop : -0.63 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.014 0.001 TYR D 436 PHE 0.017 0.001 PHE D 350 TRP 0.012 0.001 TRP D 204 HIS 0.005 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9522) covalent geometry : angle 0.59055 / 0.30 (13079) SS BOND : bond 0.00243 / 0.16 ( 5) SS BOND : angle 0.63491 / 0.30 ( 10) hydrogen bonds : bond 0.02981 / 2.20 ( 419) hydrogen bonds : angle 5.10606 / 3.79 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 292 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7876 (m-10) cc_final: 0.7619 (m-10) REVERT: D 217 THR cc_start: 0.7311 (m) cc_final: 0.7025 (p) REVERT: D 237 GLN cc_start: 0.7984 (tt0) cc_final: 0.7739 (tt0) REVERT: D 259 ILE cc_start: 0.7787 (mm) cc_final: 0.6198 (pt) REVERT: D 295 ASN cc_start: 0.8225 (p0) cc_final: 0.7989 (p0) REVERT: D 331 TYR cc_start: 0.7744 (p90) cc_final: 0.7465 (p90) REVERT: D 344 GLN cc_start: 0.7983 (pm20) cc_final: 0.7736 (pt0) REVERT: D 379 ASN cc_start: 0.8076 (t0) cc_final: 0.7604 (t0) REVERT: D 489 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 497 THR cc_start: 0.8152 (m) cc_final: 0.7927 (m) REVERT: D 503 SER cc_start: 0.8586 (m) cc_final: 0.8132 (p) REVERT: D 518 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 537 THR cc_start: 0.8020 (m) cc_final: 0.7644 (p) REVERT: D 608 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7470 (p) REVERT: D 647 GLN cc_start: 0.7516 (pt0) cc_final: 0.7167 (pt0) REVERT: D 667 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6527 (mm-40) REVERT: D 683 ASP cc_start: 0.7702 (t0) cc_final: 0.7412 (t0) REVERT: D 695 ASP cc_start: 0.6633 (p0) cc_final: 0.6373 (p0) REVERT: D 728 ASN cc_start: 0.7331 (t0) cc_final: 0.7052 (t0) REVERT: D 741 VAL cc_start: 0.8072 (t) cc_final: 0.7833 (p) REVERT: D 756 THR cc_start: 0.8641 (m) cc_final: 0.8273 (p) REVERT: D 784 ASN cc_start: 0.8018 (m-40) cc_final: 0.7253 (t0) REVERT: D 786 GLN cc_start: 0.7303 (mt0) cc_final: 0.6967 (mt0) REVERT: F 4 THR cc_start: 0.8525 (m) cc_final: 0.8194 (p) REVERT: F 123 ASN cc_start: 0.7833 (t0) cc_final: 0.7339 (t0) REVERT: C 55 PHE cc_start: 0.8200 (p90) cc_final: 0.7912 (p90) REVERT: C 57 MET cc_start: 0.5899 (mmm) cc_final: 0.5681 (mmm) REVERT: C 75 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7915 (mt) REVERT: C 105 LEU cc_start: 0.8437 (mt) cc_final: 0.8214 (mt) REVERT: C 151 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8302 (p) REVERT: H 37 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6815 (t0) REVERT: H 167 ASP cc_start: 0.7146 (t0) cc_final: 0.6884 (t0) REVERT: H 186 TYR cc_start: 0.7583 (p90) cc_final: 0.7249 (p90) REVERT: H 191 GLN cc_start: 0.8805 (pt0) cc_final: 0.8446 (pt0) outliers start: 46 outliers final: 31 residues processed: 310 average time/residue: 0.0846 time to fit residues: 38.2689 Evaluate side-chains 321 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 0.0670 chunk 110 optimal weight: 5.9990 chunk 131 optimal weight: 0.0980 chunk 129 optimal weight: 9.9990 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 257 HIS D 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106489 restraints weight = 17254.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109778 restraints weight = 9725.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111955 restraints weight = 6240.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113337 restraints weight = 4453.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114365 restraints weight = 3488.495| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9527 Z= 0.094 Angle : 0.602 13.742 13089 Z= 0.300 Chirality : 0.046 0.171 1569 Planarity : 0.004 0.061 1758 Dihedral : 3.518 17.631 1519 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.69 % Allowed : 34.99 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.08 (0.23), residues: 1424 helix: -1.38 (0.83), residues: 44 sheet: 0.92 (0.21), residues: 618 loop : -0.58 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 116 TYR 0.018 0.001 TYR D 366 PHE 0.013 0.001 PHE D 380 TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 9522) covalent geometry : angle 0.60203 / 0.30 (13079) SS BOND : bond 0.00261 / 0.17 ( 5) SS BOND : angle 0.61231 / 0.30 ( 10) hydrogen bonds : bond 0.02744 / 2.03 ( 419) hydrogen bonds : angle 4.94969 / 3.68 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 0.412 Fit side-chains REVERT: D 217 THR cc_start: 0.7269 (m) cc_final: 0.7001 (p) REVERT: D 237 GLN cc_start: 0.7935 (tt0) cc_final: 0.7722 (tt0) REVERT: D 259 ILE cc_start: 0.7722 (mm) cc_final: 0.6138 (pt) REVERT: D 312 ILE cc_start: 0.8652 (mp) cc_final: 0.8452 (mp) REVERT: D 323 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6725 (tp) REVERT: D 331 TYR cc_start: 0.7810 (p90) cc_final: 0.7442 (p90) REVERT: D 379 ASN cc_start: 0.8087 (t0) cc_final: 0.7577 (t0) REVERT: D 489 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7932 (p) REVERT: D 497 THR cc_start: 0.8142 (m) cc_final: 0.7915 (m) REVERT: D 518 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 531 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7246 (p) REVERT: D 537 THR cc_start: 0.8003 (m) cc_final: 0.7653 (p) REVERT: D 599 ASP cc_start: 0.8007 (t0) cc_final: 0.7695 (t0) REVERT: D 608 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7426 (p) REVERT: D 647 GLN cc_start: 0.7460 (pt0) cc_final: 0.7110 (pt0) REVERT: D 683 ASP cc_start: 0.7578 (t0) cc_final: 0.7296 (t0) REVERT: D 695 ASP cc_start: 0.6501 (p0) cc_final: 0.6245 (p0) REVERT: D 708 TYR cc_start: 0.8058 (m-10) cc_final: 0.7758 (m-10) REVERT: D 728 ASN cc_start: 0.7286 (t0) cc_final: 0.6916 (t0) REVERT: D 741 VAL cc_start: 0.8040 (t) cc_final: 0.7791 (p) REVERT: D 756 THR cc_start: 0.8692 (m) cc_final: 0.8316 (p) REVERT: D 784 ASN cc_start: 0.7939 (m-40) cc_final: 0.7267 (t0) REVERT: D 786 GLN cc_start: 0.7269 (mt0) cc_final: 0.6917 (mt0) REVERT: F 4 THR cc_start: 0.8583 (m) cc_final: 0.8219 (p) REVERT: F 123 ASN cc_start: 0.7794 (t0) cc_final: 0.7292 (t0) REVERT: C 55 PHE cc_start: 0.8059 (p90) cc_final: 0.7703 (p90) REVERT: C 75 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7838 (mt) REVERT: C 151 THR cc_start: 0.8610 (m) cc_final: 0.8319 (p) REVERT: H 37 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6801 (t0) REVERT: H 167 ASP cc_start: 0.7048 (t0) cc_final: 0.6762 (t0) REVERT: H 186 TYR cc_start: 0.7463 (p90) cc_final: 0.7163 (p90) REVERT: H 191 GLN cc_start: 0.8752 (pt0) cc_final: 0.8425 (pt0) REVERT: H 236 ASN cc_start: 0.8823 (t0) cc_final: 0.8397 (t0) outliers start: 39 outliers final: 28 residues processed: 307 average time/residue: 0.0823 time to fit residues: 36.8334 Evaluate side-chains 313 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102929 restraints weight = 17520.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106440 restraints weight = 9780.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108786 restraints weight = 6261.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110415 restraints weight = 4472.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111386 restraints weight = 3475.367| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9527 Z= 0.119 Angle : 0.611 13.391 13089 Z= 0.305 Chirality : 0.045 0.173 1569 Planarity : 0.004 0.059 1758 Dihedral : 3.609 17.135 1519 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.54 % Allowed : 35.57 % Favored : 58.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.11 (0.23), residues: 1424 helix: -1.36 (0.82), residues: 44 sheet: 0.93 (0.21), residues: 616 loop : -0.55 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.018 0.001 TYR D 366 PHE 0.020 0.002 PHE D 350 TRP 0.011 0.001 TRP D 204 HIS 0.005 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9522) covalent geometry : angle 0.61061 / 0.30 (13079) SS BOND : bond 0.00304 / 0.18 ( 5) SS BOND : angle 0.60069 / 0.30 ( 10) hydrogen bonds : bond 0.02921 / 2.16 ( 419) hydrogen bonds : angle 5.00906 / 3.72 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.398 Fit side-chains REVERT: D 134 ASP cc_start: 0.7442 (t0) cc_final: 0.7142 (t0) REVERT: D 259 ILE cc_start: 0.7820 (mm) cc_final: 0.6287 (pt) REVERT: D 331 TYR cc_start: 0.7776 (p90) cc_final: 0.7413 (p90) REVERT: D 344 GLN cc_start: 0.8107 (pm20) cc_final: 0.7853 (pt0) REVERT: D 374 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7500 (ttm110) REVERT: D 379 ASN cc_start: 0.8066 (t0) cc_final: 0.7585 (t0) REVERT: D 382 ILE cc_start: 0.8040 (mp) cc_final: 0.7706 (mm) REVERT: D 489 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.7942 (p) REVERT: D 494 ARG cc_start: 0.7194 (tpp-160) cc_final: 0.6932 (tpp-160) REVERT: D 497 THR cc_start: 0.8130 (m) cc_final: 0.7929 (m) REVERT: D 518 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 531 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7279 (p) REVERT: D 537 THR cc_start: 0.8034 (m) cc_final: 0.7665 (p) REVERT: D 608 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7482 (p) REVERT: D 647 GLN cc_start: 0.7485 (pt0) cc_final: 0.7014 (pt0) REVERT: D 683 ASP cc_start: 0.7740 (t0) cc_final: 0.7396 (t0) REVERT: D 695 ASP cc_start: 0.6684 (p0) cc_final: 0.6381 (p0) REVERT: D 728 ASN cc_start: 0.7379 (t0) cc_final: 0.6993 (t0) REVERT: D 741 VAL cc_start: 0.8080 (t) cc_final: 0.7711 (p) REVERT: D 756 THR cc_start: 0.8615 (m) cc_final: 0.8028 (p) REVERT: D 784 ASN cc_start: 0.8025 (m-40) cc_final: 0.7267 (t0) REVERT: D 786 GLN cc_start: 0.7294 (mt0) cc_final: 0.6959 (mt0) REVERT: F 4 THR cc_start: 0.8499 (m) cc_final: 0.8163 (p) REVERT: F 123 ASN cc_start: 0.7879 (t0) cc_final: 0.7377 (t0) REVERT: C 55 PHE cc_start: 0.8112 (p90) cc_final: 0.7709 (p90) REVERT: C 57 MET cc_start: 0.5407 (mmm) cc_final: 0.5101 (mmm) REVERT: C 75 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7899 (mt) REVERT: C 151 THR cc_start: 0.8656 (m) cc_final: 0.8323 (p) REVERT: H 37 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6816 (t0) REVERT: H 167 ASP cc_start: 0.7093 (t0) cc_final: 0.6833 (t0) REVERT: H 186 TYR cc_start: 0.7527 (p90) cc_final: 0.7190 (p90) REVERT: H 191 GLN cc_start: 0.8868 (pt0) cc_final: 0.8481 (pt0) outliers start: 38 outliers final: 30 residues processed: 304 average time/residue: 0.0844 time to fit residues: 37.2736 Evaluate side-chains 316 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 136 optimal weight: 0.0270 chunk 93 optimal weight: 30.0000 chunk 36 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 237 GLN D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107154 restraints weight = 17005.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110273 restraints weight = 9590.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112493 restraints weight = 6266.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114010 restraints weight = 4539.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114921 restraints weight = 3565.658| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9527 Z= 0.167 Angle : 0.644 12.825 13089 Z= 0.328 Chirality : 0.046 0.186 1569 Planarity : 0.004 0.060 1758 Dihedral : 3.919 18.664 1519 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 6.27 % Allowed : 34.55 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.05 (0.22), residues: 1424 helix: -1.48 (0.82), residues: 44 sheet: 0.84 (0.21), residues: 613 loop : -0.67 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 66 TYR 0.018 0.002 TYR D 366 PHE 0.015 0.002 PHE C 55 TRP 0.015 0.002 TRP D 204 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9522) covalent geometry : angle 0.64407 / 0.33 (13079) SS BOND : bond 0.00219 / 0.14 ( 5) SS BOND : angle 0.57659 / 0.29 ( 10) hydrogen bonds : bond 0.03279 / 2.43 ( 419) hydrogen bonds : angle 5.20479 / 3.86 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.333 Fit side-chains REVERT: D 213 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7683 (tpp80) REVERT: D 259 ILE cc_start: 0.7867 (mm) cc_final: 0.6355 (pt) REVERT: D 331 TYR cc_start: 0.7755 (p90) cc_final: 0.7408 (p90) REVERT: D 344 GLN cc_start: 0.8146 (pm20) cc_final: 0.7900 (pt0) REVERT: D 374 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7520 (ttm110) REVERT: D 379 ASN cc_start: 0.7998 (t0) cc_final: 0.7409 (t0) REVERT: D 382 ILE cc_start: 0.8111 (mp) cc_final: 0.7791 (mm) REVERT: D 489 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8004 (p) REVERT: D 494 ARG cc_start: 0.7367 (tpp-160) cc_final: 0.7102 (tpp-160) REVERT: D 503 SER cc_start: 0.8601 (m) cc_final: 0.8187 (p) REVERT: D 518 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 532 LEU cc_start: 0.8643 (tp) cc_final: 0.8380 (tp) REVERT: D 537 THR cc_start: 0.8043 (m) cc_final: 0.7681 (p) REVERT: D 557 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: D 608 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7443 (p) REVERT: D 647 GLN cc_start: 0.7485 (pt0) cc_final: 0.7027 (pt0) REVERT: D 683 ASP cc_start: 0.7765 (t0) cc_final: 0.7427 (t0) REVERT: D 695 ASP cc_start: 0.6719 (p0) cc_final: 0.6409 (p0) REVERT: D 728 ASN cc_start: 0.7400 (t0) cc_final: 0.7068 (t0) REVERT: D 745 PHE cc_start: 0.7609 (m-80) cc_final: 0.7275 (m-80) REVERT: D 756 THR cc_start: 0.8640 (m) cc_final: 0.8314 (p) REVERT: D 784 ASN cc_start: 0.8002 (m-40) cc_final: 0.7381 (t0) REVERT: D 786 GLN cc_start: 0.7269 (mt0) cc_final: 0.6951 (mt0) REVERT: F 4 THR cc_start: 0.8508 (m) cc_final: 0.8191 (p) REVERT: F 123 ASN cc_start: 0.7950 (t0) cc_final: 0.7436 (t0) REVERT: C 55 PHE cc_start: 0.8208 (p90) cc_final: 0.7885 (p90) REVERT: C 57 MET cc_start: 0.5566 (mmm) cc_final: 0.5242 (mmm) REVERT: C 151 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8294 (p) REVERT: H 37 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6822 (t0) REVERT: H 167 ASP cc_start: 0.7141 (t0) cc_final: 0.6865 (t0) REVERT: H 186 TYR cc_start: 0.7564 (p90) cc_final: 0.7239 (p90) REVERT: H 191 GLN cc_start: 0.8804 (pt0) cc_final: 0.8442 (pt0) outliers start: 43 outliers final: 31 residues processed: 301 average time/residue: 0.0823 time to fit residues: 36.0332 Evaluate side-chains 311 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 76 optimal weight: 0.0020 chunk 122 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 237 GLN D 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107084 restraints weight = 17439.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110415 restraints weight = 9839.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112666 restraints weight = 6373.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114139 restraints weight = 4586.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115203 restraints weight = 3617.635| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9527 Z= 0.155 Angle : 0.656 13.209 13089 Z= 0.330 Chirality : 0.046 0.183 1569 Planarity : 0.004 0.058 1758 Dihedral : 3.935 20.607 1519 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.39 % Allowed : 36.44 % Favored : 58.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.09 (0.22), residues: 1424 helix: -1.47 (0.82), residues: 44 sheet: 0.85 (0.21), residues: 607 loop : -0.71 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.019 0.002 TYR D 366 PHE 0.022 0.002 PHE D 350 TRP 0.014 0.002 TRP C 36 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 9522) covalent geometry : angle 0.65588 / 0.33 (13079) SS BOND : bond 0.00234 / 0.15 ( 5) SS BOND : angle 0.58109 / 0.28 ( 10) hydrogen bonds : bond 0.03166 / 2.33 ( 419) hydrogen bonds : angle 5.18706 / 3.86 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.347 Fit side-chains REVERT: D 213 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7708 (tpp80) REVERT: D 259 ILE cc_start: 0.7882 (mm) cc_final: 0.6380 (pt) REVERT: D 331 TYR cc_start: 0.7735 (p90) cc_final: 0.7392 (p90) REVERT: D 344 GLN cc_start: 0.8155 (pm20) cc_final: 0.7933 (pt0) REVERT: D 374 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7526 (ttm110) REVERT: D 379 ASN cc_start: 0.7983 (t0) cc_final: 0.7381 (t0) REVERT: D 382 ILE cc_start: 0.8117 (mp) cc_final: 0.7882 (mm) REVERT: D 489 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7996 (p) REVERT: D 494 ARG cc_start: 0.7425 (tpp-160) cc_final: 0.7148 (tpp-160) REVERT: D 497 THR cc_start: 0.8218 (m) cc_final: 0.7984 (m) REVERT: D 503 SER cc_start: 0.8617 (m) cc_final: 0.8197 (p) REVERT: D 518 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 531 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7390 (p) REVERT: D 537 THR cc_start: 0.8051 (m) cc_final: 0.7686 (p) REVERT: D 557 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7741 (m-10) REVERT: D 608 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7441 (p) REVERT: D 647 GLN cc_start: 0.7489 (pt0) cc_final: 0.7032 (pt0) REVERT: D 683 ASP cc_start: 0.7790 (t0) cc_final: 0.7442 (t0) REVERT: D 695 ASP cc_start: 0.6766 (p0) cc_final: 0.6452 (p0) REVERT: D 728 ASN cc_start: 0.7431 (t0) cc_final: 0.7055 (t0) REVERT: D 756 THR cc_start: 0.8625 (m) cc_final: 0.8291 (p) REVERT: D 770 VAL cc_start: 0.8217 (m) cc_final: 0.7942 (t) REVERT: D 784 ASN cc_start: 0.8031 (m-40) cc_final: 0.7441 (t0) REVERT: D 786 GLN cc_start: 0.7246 (mt0) cc_final: 0.6879 (mt0) REVERT: F 4 THR cc_start: 0.8526 (m) cc_final: 0.8203 (p) REVERT: F 123 ASN cc_start: 0.7893 (t0) cc_final: 0.7388 (t0) REVERT: C 49 ILE cc_start: 0.8538 (mm) cc_final: 0.8314 (mm) REVERT: C 55 PHE cc_start: 0.8168 (p90) cc_final: 0.7897 (p90) REVERT: C 57 MET cc_start: 0.5602 (mmm) cc_final: 0.5271 (mmm) REVERT: C 151 THR cc_start: 0.8679 (m) cc_final: 0.8307 (p) REVERT: H 37 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6843 (t0) REVERT: H 167 ASP cc_start: 0.7118 (t0) cc_final: 0.6869 (t0) REVERT: H 186 TYR cc_start: 0.7582 (p90) cc_final: 0.7249 (p90) REVERT: H 191 GLN cc_start: 0.8798 (pt0) cc_final: 0.8477 (pt0) outliers start: 37 outliers final: 31 residues processed: 298 average time/residue: 0.0847 time to fit residues: 36.5274 Evaluate side-chains 311 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 489 THR Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 557 PHE Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain F residue 56 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 TYR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 111 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107414 restraints weight = 17329.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110742 restraints weight = 9785.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112973 restraints weight = 6355.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114482 restraints weight = 4585.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115327 restraints weight = 3605.132| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9527 Z= 0.146 Angle : 0.651 13.180 13089 Z= 0.328 Chirality : 0.046 0.180 1569 Planarity : 0.004 0.059 1758 Dihedral : 3.927 20.519 1519 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.83 % Allowed : 36.01 % Favored : 58.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.08 (0.22), residues: 1424 helix: -1.44 (0.82), residues: 44 sheet: 0.79 (0.21), residues: 615 loop : -0.67 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 116 TYR 0.018 0.002 TYR D 366 PHE 0.013 0.002 PHE D 380 TRP 0.013 0.002 TRP D 204 HIS 0.006 0.001 HIS D 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9522) covalent geometry : angle 0.65097 / 0.33 (13079) SS BOND : bond 0.00231 / 0.15 ( 5) SS BOND : angle 0.56196 / 0.27 ( 10) hydrogen bonds : bond 0.03116 / 2.31 ( 419) hydrogen bonds : angle 5.17886 / 3.86 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.40 seconds wall clock time: 30 minutes 33.28 seconds (1833.28 seconds total)