Starting phenix.real_space_refine on Wed Apr 30 09:50:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_44735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_44735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_44735.map" model { file = "/net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_44735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bog_44735/04_2025/9bog_44735.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 16, 'HIS:plan': 5, 'TYR:plan': 8, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} 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: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG: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: {'GLN:plan1': 2, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'GLN:plan1': 7, 'ARG:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 251 Time building chain proxies: 6.14, per 1000 atoms: 0.66 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: 2.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.64 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: 3.96 Time building geometry restraints manager: 2.71 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP D 508 HIS 0.007 0.001 HIS D 809 PHE 0.008 0.001 PHE D 525 TYR 0.014 0.001 TYR D 593 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.14610 ( 419) hydrogen bonds : angle 6.25196 ( 1083) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.08155 ( 10) covalent geometry : bond 0.00193 ( 9522) covalent geometry : angle 0.53628 (13079) *********************** 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 : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 257 HIS cc_start: 0.6899 (m-70) cc_final: 0.6330 (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: 0.6879 (p) REVERT: D 379 ASN cc_start: 0.7299 (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: 0.8111 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 531 THR cc_start: 0.7266 (t) cc_final: 0.6974 (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: 0.6978 (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: 0.7544 (p0) REVERT: D 669 LEU cc_start: 0.8051 (mp) cc_final: 0.7797 (mt) REVERT: D 688 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7169 (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: 0.6990 (mt0) REVERT: D 829 SER cc_start: 0.8534 (t) cc_final: 0.8167 (p) REVERT: F 4 THR cc_start: 0.8555 (m) cc_final: 0.8203 (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: 0.7723 (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: 0.8962 (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: 0.2076 time to fit residues: 89.3929 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 : 0.896 ------------------------------------------------------------------------------- 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 119 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3701 r_free = 0.3701 target = 0.133741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107564 restraints weight = 17614.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111063 restraints weight = 9695.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113393 restraints weight = 6179.439| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 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 = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9527 Z= 0.112 Angle : 0.562 10.091 13089 Z= 0.287 Chirality : 0.044 0.162 1569 Planarity : 0.004 0.060 1758 Dihedral : 3.296 16.957 1521 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 8.16 % Allowed : 29.01 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1424 helix: -1.75 (0.80), residues: 44 sheet: 0.85 (0.20), residues: 642 loop : -0.29 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS D 504 PHE 0.011 0.001 PHE D 4 TYR 0.016 0.001 TYR D 650 ARG 0.006 0.001 ARG H 258 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 419) hydrogen bonds : angle 5.15104 ( 1083) SS BOND : bond 0.00371 ( 5) SS BOND : angle 0.88509 ( 10) covalent geometry : bond 0.00242 ( 9522) covalent geometry : angle 0.56211 (13079) *********************** 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 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: D 237 GLN cc_start: 0.8015 (tt0) cc_final: 0.7797 (tt0) REVERT: D 257 HIS cc_start: 0.7173 (m-70) cc_final: 0.6813 (m90) REVERT: D 324 GLN cc_start: 0.6691 (mm-40) cc_final: 0.6333 (mm110) REVERT: D 332 SER cc_start: 0.7667 (t) cc_final: 0.7337 (p) REVERT: D 346 GLU cc_start: 0.7078 (mp0) cc_final: 0.6777 (mp0) REVERT: D 379 ASN cc_start: 0.7925 (t0) cc_final: 0.7502 (t0) REVERT: D 489 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7881 (p) REVERT: D 518 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 523 THR cc_start: 0.5852 (OUTLIER) cc_final: 0.5641 (t) REVERT: D 531 THR cc_start: 0.7472 (t) cc_final: 0.7092 (p) REVERT: D 537 THR cc_start: 0.7982 (m) cc_final: 0.7643 (p) REVERT: D 588 ASN cc_start: 0.8285 (m-40) cc_final: 0.8026 (m-40) REVERT: D 599 ASP cc_start: 0.7863 (t0) cc_final: 0.7516 (t0) REVERT: D 608 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7496 (p) REVERT: D 647 GLN cc_start: 0.7478 (pt0) cc_final: 0.7079 (pt0) REVERT: D 669 LEU cc_start: 0.8480 (mp) cc_final: 0.8224 (mt) REVERT: D 688 ASN cc_start: 0.7887 (m110) cc_final: 0.7636 (m110) REVERT: D 706 THR cc_start: 0.8017 (p) cc_final: 0.7725 (t) REVERT: D 741 VAL cc_start: 0.7995 (t) cc_final: 0.7650 (p) REVERT: D 786 GLN cc_start: 0.7429 (mt0) cc_final: 0.7104 (mt0) REVERT: F 4 THR cc_start: 0.8566 (m) cc_final: 0.8197 (p) REVERT: F 123 ASN cc_start: 0.7849 (t0) cc_final: 0.7366 (t0) REVERT: C 4 LEU cc_start: 0.8488 (mt) cc_final: 0.8252 (mp) REVERT: C 57 MET cc_start: 0.6202 (mmm) cc_final: 0.5937 (mpp) REVERT: C 75 LEU cc_start: 0.8229 (mm) cc_final: 0.7945 (mt) REVERT: C 151 THR cc_start: 0.8612 (m) cc_final: 0.8198 (p) REVERT: H 37 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6592 (t0) REVERT: H 167 ASP cc_start: 0.7382 (t0) cc_final: 0.7115 (t0) REVERT: H 186 TYR cc_start: 0.7615 (p90) cc_final: 0.7311 (p90) REVERT: H 191 GLN cc_start: 0.8960 (pt0) cc_final: 0.8551 (pt0) REVERT: H 219 GLN cc_start: 0.8236 (pm20) cc_final: 0.7986 (pm20) REVERT: H 269 GLN cc_start: 0.8255 (tt0) cc_final: 0.7454 (tt0) outliers start: 56 outliers final: 26 residues processed: 308 average time/residue: 0.1808 time to fit residues: 80.2206 Evaluate side-chains 297 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 523 THR 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 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 61 LYS 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 105 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.0030 chunk 120 optimal weight: 20.0000 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101998 restraints weight = 17580.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105261 restraints weight = 9669.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107431 restraints weight = 6147.811| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9527 Z= 0.228 Angle : 0.633 12.166 13089 Z= 0.332 Chirality : 0.046 0.199 1569 Planarity : 0.004 0.063 1758 Dihedral : 3.990 18.004 1519 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 8.16 % Allowed : 31.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1424 helix: -1.80 (0.73), residues: 44 sheet: 0.77 (0.21), residues: 639 loop : -0.46 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 204 HIS 0.024 0.004 HIS D 809 PHE 0.027 0.002 PHE C 55 TYR 0.024 0.002 TYR D 338 ARG 0.007 0.001 ARG D 709 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 419) hydrogen bonds : angle 5.38603 ( 1083) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.91214 ( 10) covalent geometry : bond 0.00477 ( 9522) covalent geometry : angle 0.63225 (13079) *********************** 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 348 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: D 324 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6600 (mm110) REVERT: D 328 HIS cc_start: 0.8143 (t-90) cc_final: 0.7928 (t-90) REVERT: D 379 ASN cc_start: 0.7887 (t0) cc_final: 0.7428 (t0) REVERT: D 382 ILE cc_start: 0.8224 (mp) cc_final: 0.7866 (mm) REVERT: D 386 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6878 (mtp) REVERT: D 416 PHE cc_start: 0.7396 (m-80) cc_final: 0.7190 (m-10) REVERT: D 484 LEU cc_start: 0.8542 (tp) cc_final: 0.8319 (tt) REVERT: D 489 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8001 (p) REVERT: D 503 SER cc_start: 0.8585 (m) cc_final: 0.8094 (p) REVERT: D 518 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 537 THR cc_start: 0.7970 (m) cc_final: 0.7638 (p) REVERT: D 557 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7858 (m-10) REVERT: D 576 TYR cc_start: 0.7551 (t80) cc_final: 0.7302 (t80) REVERT: D 588 ASN cc_start: 0.8184 (m-40) cc_final: 0.7826 (m-40) REVERT: D 599 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (t0) REVERT: D 608 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7458 (p) REVERT: D 634 ASN cc_start: 0.7960 (m110) cc_final: 0.6451 (m110) REVERT: D 647 GLN cc_start: 0.7522 (pt0) cc_final: 0.7135 (pt0) REVERT: D 683 ASP cc_start: 0.7756 (t0) cc_final: 0.7424 (t0) REVERT: D 688 ASN cc_start: 0.7966 (m110) cc_final: 0.7710 (m110) REVERT: D 741 VAL cc_start: 0.8206 (t) cc_final: 0.7988 (p) REVERT: D 786 GLN cc_start: 0.7352 (mt0) cc_final: 0.7079 (mt0) REVERT: F 4 THR cc_start: 0.8554 (m) cc_final: 0.8217 (p) REVERT: F 64 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8063 (mttm) REVERT: F 65 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8709 (p) REVERT: F 115 THR cc_start: 0.8633 (m) cc_final: 0.8342 (t) REVERT: F 123 ASN cc_start: 0.7988 (t0) cc_final: 0.7456 (t0) REVERT: C 55 PHE cc_start: 0.8184 (p90) cc_final: 0.7863 (p90) REVERT: C 57 MET cc_start: 0.6221 (mmm) cc_final: 0.5738 (mmm) REVERT: C 75 LEU cc_start: 0.8298 (mm) cc_final: 0.7989 (mt) REVERT: C 151 THR cc_start: 0.8668 (m) cc_final: 0.8227 (p) REVERT: H 37 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6586 (t0) REVERT: H 167 ASP cc_start: 0.7382 (t0) cc_final: 0.7058 (t0) REVERT: H 186 TYR cc_start: 0.7694 (p90) cc_final: 0.7403 (p90) REVERT: H 191 GLN cc_start: 0.8928 (pt0) cc_final: 0.8511 (pt0) REVERT: H 269 GLN cc_start: 0.8381 (tt0) cc_final: 0.8087 (tt0) outliers start: 56 outliers final: 32 residues processed: 312 average time/residue: 0.1885 time to fit residues: 83.4567 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 : 0.930 ------------------------------------------------------------------------------- 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 216 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 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 685 LYS 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 16 CYS 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 50 VAL 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 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 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 53 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 12 optimal weight: 0.0030 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN D 257 HIS D 667 GLN C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102214 restraints weight = 17360.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105512 restraints weight = 9572.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107561 restraints weight = 6097.661| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9527 Z= 0.179 Angle : 0.601 9.072 13089 Z= 0.313 Chirality : 0.046 0.306 1569 Planarity : 0.004 0.056 1758 Dihedral : 3.940 18.180 1519 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.71 % Allowed : 32.65 % Favored : 60.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1424 helix: -1.57 (0.78), residues: 44 sheet: 0.69 (0.20), residues: 645 loop : -0.54 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 204 HIS 0.008 0.002 HIS D 659 PHE 0.032 0.002 PHE D 745 TYR 0.019 0.002 TYR D 338 ARG 0.004 0.001 ARG D 709 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 419) hydrogen bonds : angle 5.34697 ( 1083) SS BOND : bond 0.00357 ( 5) SS BOND : angle 0.67356 ( 10) covalent geometry : bond 0.00381 ( 9522) covalent geometry : angle 0.60097 (13079) *********************** 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 336 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: D 323 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7417 (mm) REVERT: D 324 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6481 (mm110) REVERT: D 379 ASN cc_start: 0.7931 (t0) cc_final: 0.7405 (t0) REVERT: D 386 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6953 (mtp) REVERT: D 442 PHE cc_start: 0.7484 (m-80) cc_final: 0.7210 (m-10) REVERT: D 484 LEU cc_start: 0.8546 (tp) cc_final: 0.8319 (tt) REVERT: D 489 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8024 (p) REVERT: D 503 SER cc_start: 0.8589 (m) cc_final: 0.8147 (p) REVERT: D 518 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7827 (tm-30) REVERT: D 532 LEU cc_start: 0.8725 (tp) cc_final: 0.8467 (tp) REVERT: D 537 THR cc_start: 0.8000 (m) cc_final: 0.7681 (p) REVERT: D 588 ASN cc_start: 0.8175 (m-40) cc_final: 0.7745 (m-40) REVERT: D 599 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7813 (t0) REVERT: D 608 THR cc_start: 0.7909 (t) cc_final: 0.7408 (p) REVERT: D 647 GLN cc_start: 0.7518 (pt0) cc_final: 0.7166 (pt0) REVERT: D 652 VAL cc_start: 0.8385 (m) cc_final: 0.8148 (p) REVERT: D 683 ASP cc_start: 0.7726 (t0) cc_final: 0.7407 (t0) REVERT: D 688 ASN cc_start: 0.8042 (m110) cc_final: 0.7790 (m110) REVERT: D 728 ASN cc_start: 0.7404 (t0) cc_final: 0.7197 (t0) REVERT: D 741 VAL cc_start: 0.8183 (t) cc_final: 0.7981 (p) REVERT: D 756 THR cc_start: 0.8721 (m) cc_final: 0.8090 (p) REVERT: D 784 ASN cc_start: 0.8029 (m-40) cc_final: 0.7340 (t0) REVERT: D 786 GLN cc_start: 0.7355 (mt0) cc_final: 0.7025 (mt0) REVERT: F 4 THR cc_start: 0.8533 (m) cc_final: 0.8219 (p) REVERT: F 64 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8026 (mttm) REVERT: F 65 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8704 (p) REVERT: F 115 THR cc_start: 0.8673 (m) cc_final: 0.8338 (t) REVERT: F 123 ASN cc_start: 0.7937 (t0) cc_final: 0.7424 (t0) REVERT: C 55 PHE cc_start: 0.8161 (p90) cc_final: 0.7841 (p90) REVERT: C 57 MET cc_start: 0.6283 (mmm) cc_final: 0.5932 (mmm) REVERT: C 75 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7929 (mt) REVERT: C 151 THR cc_start: 0.8663 (m) cc_final: 0.8269 (p) REVERT: H 37 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6794 (t0) REVERT: H 167 ASP cc_start: 0.7340 (t0) cc_final: 0.7072 (t0) REVERT: H 186 TYR cc_start: 0.7700 (p90) cc_final: 0.7330 (p90) REVERT: H 191 GLN cc_start: 0.8869 (pt0) cc_final: 0.8514 (pt0) REVERT: H 227 ARG cc_start: 0.8696 (ttt-90) cc_final: 0.8466 (ttt-90) outliers start: 46 outliers final: 30 residues processed: 310 average time/residue: 0.1887 time to fit residues: 83.0896 Evaluate side-chains 324 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 240 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 386 MET 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 599 ASP Chi-restraints excluded: chain D residue 685 LYS 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 23 THR 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 191 ASN Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 172 LEU 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 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3625 r_free = 0.3625 target = 0.128604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102923 restraints weight = 17551.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106312 restraints weight = 9769.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108578 restraints weight = 6263.116| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2900 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= 0.130 Angle : 0.579 8.663 13089 Z= 0.300 Chirality : 0.046 0.225 1569 Planarity : 0.004 0.087 1758 Dihedral : 3.784 18.386 1519 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 7.43 % Allowed : 32.80 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1424 helix: -1.42 (0.81), residues: 44 sheet: 0.79 (0.21), residues: 630 loop : -0.62 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 183 HIS 0.006 0.001 HIS D 659 PHE 0.019 0.002 PHE C 55 TYR 0.013 0.001 TYR D 650 ARG 0.004 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 419) hydrogen bonds : angle 5.17603 ( 1083) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.62466 ( 10) covalent geometry : bond 0.00284 ( 9522) covalent geometry : angle 0.57916 (13079) *********************** 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 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7915 (m-10) cc_final: 0.7623 (m-10) REVERT: D 210 ILE cc_start: 0.8817 (mm) cc_final: 0.8581 (mm) REVERT: D 213 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7704 (tpp80) REVERT: D 259 ILE cc_start: 0.7778 (mm) cc_final: 0.6142 (pt) REVERT: D 295 ASN cc_start: 0.8225 (p0) cc_final: 0.7978 (p0) REVERT: D 323 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7339 (mm) REVERT: D 324 GLN cc_start: 0.6696 (mm-40) cc_final: 0.6403 (mm110) REVERT: D 379 ASN cc_start: 0.8066 (t0) cc_final: 0.7663 (t0) REVERT: D 382 ILE cc_start: 0.8152 (mp) cc_final: 0.7849 (mm) REVERT: D 394 VAL cc_start: 0.8115 (p) cc_final: 0.7839 (m) REVERT: D 442 PHE cc_start: 0.7604 (m-80) cc_final: 0.7352 (m-10) REVERT: D 448 THR cc_start: 0.8247 (p) cc_final: 0.8002 (p) REVERT: D 489 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8019 (p) REVERT: D 503 SER cc_start: 0.8579 (m) cc_final: 0.8119 (p) REVERT: D 518 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 532 LEU cc_start: 0.8642 (tp) cc_final: 0.8426 (tp) REVERT: D 537 THR cc_start: 0.7996 (m) cc_final: 0.7679 (p) REVERT: D 588 ASN cc_start: 0.8142 (m-40) cc_final: 0.7725 (m-40) REVERT: D 599 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7774 (t0) REVERT: D 608 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7490 (p) REVERT: D 647 GLN cc_start: 0.7484 (pt0) cc_final: 0.7137 (pt0) REVERT: D 652 VAL cc_start: 0.8320 (m) cc_final: 0.8098 (p) REVERT: D 683 ASP cc_start: 0.7654 (t0) cc_final: 0.7329 (t0) REVERT: D 688 ASN cc_start: 0.8029 (m110) cc_final: 0.7755 (m110) REVERT: D 695 ASP cc_start: 0.6620 (p0) cc_final: 0.6410 (p0) REVERT: D 728 ASN cc_start: 0.7441 (t0) cc_final: 0.7140 (t0) REVERT: D 741 VAL cc_start: 0.8096 (t) cc_final: 0.7864 (p) REVERT: D 756 THR cc_start: 0.8693 (m) cc_final: 0.8074 (p) REVERT: D 784 ASN cc_start: 0.8013 (m-40) cc_final: 0.7326 (t0) REVERT: D 786 GLN cc_start: 0.7289 (mt0) cc_final: 0.6978 (mt0) REVERT: F 4 THR cc_start: 0.8541 (m) cc_final: 0.8178 (p) REVERT: F 65 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8681 (p) REVERT: F 123 ASN cc_start: 0.7821 (t0) cc_final: 0.7299 (t0) REVERT: C 55 PHE cc_start: 0.8171 (p90) cc_final: 0.7864 (p90) REVERT: C 57 MET cc_start: 0.6374 (mmm) cc_final: 0.6069 (mmm) REVERT: C 75 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 151 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8331 (p) REVERT: H 37 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6828 (t0) REVERT: H 167 ASP cc_start: 0.7336 (t0) cc_final: 0.7018 (t0) REVERT: H 186 TYR cc_start: 0.7658 (p90) cc_final: 0.7279 (p90) REVERT: H 191 GLN cc_start: 0.8823 (pt0) cc_final: 0.8446 (pt0) outliers start: 51 outliers final: 35 residues processed: 308 average time/residue: 0.2159 time to fit residues: 96.3728 Evaluate side-chains 326 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 323 LEU Chi-restraints excluded: chain D residue 338 TYR 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 599 ASP 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 685 LYS 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 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 C residue 10 ILE Chi-restraints excluded: chain C residue 11 TYR 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 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 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 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 113 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.126585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100373 restraints weight = 17496.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103759 restraints weight = 9706.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106028 restraints weight = 6240.842| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9527 Z= 0.165 Angle : 0.607 8.278 13089 Z= 0.313 Chirality : 0.046 0.193 1569 Planarity : 0.004 0.077 1758 Dihedral : 3.895 19.242 1519 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 7.14 % Allowed : 33.82 % Favored : 59.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1424 helix: -1.46 (0.80), residues: 44 sheet: 0.75 (0.21), residues: 621 loop : -0.64 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 204 HIS 0.006 0.001 HIS D 659 PHE 0.017 0.002 PHE C 55 TYR 0.016 0.002 TYR D 338 ARG 0.004 0.000 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 419) hydrogen bonds : angle 5.25809 ( 1083) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.64694 ( 10) covalent geometry : bond 0.00354 ( 9522) covalent geometry : angle 0.60651 (13079) *********************** 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 332 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7913 (m-10) cc_final: 0.7650 (m-10) REVERT: D 210 ILE cc_start: 0.8816 (mm) cc_final: 0.8582 (mm) REVERT: D 259 ILE cc_start: 0.7823 (mm) cc_final: 0.6249 (pt) REVERT: D 295 ASN cc_start: 0.8229 (p0) cc_final: 0.7988 (p0) REVERT: D 323 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7353 (mm) REVERT: D 324 GLN cc_start: 0.6785 (mm-40) cc_final: 0.6496 (mm110) REVERT: D 344 GLN cc_start: 0.8008 (pm20) cc_final: 0.7772 (pt0) REVERT: D 379 ASN cc_start: 0.7950 (t0) cc_final: 0.7395 (t0) REVERT: D 382 ILE cc_start: 0.8118 (mp) cc_final: 0.7862 (mm) REVERT: D 442 PHE cc_start: 0.7668 (m-80) cc_final: 0.7456 (m-10) REVERT: D 489 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 503 SER cc_start: 0.8581 (m) cc_final: 0.8139 (p) REVERT: D 518 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7830 (tm-30) REVERT: D 532 LEU cc_start: 0.8673 (tp) cc_final: 0.8449 (tp) REVERT: D 537 THR cc_start: 0.8043 (m) cc_final: 0.7702 (p) REVERT: D 588 ASN cc_start: 0.8104 (m-40) cc_final: 0.7655 (m-40) REVERT: D 599 ASP cc_start: 0.8072 (t70) cc_final: 0.7835 (t0) REVERT: D 608 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7493 (p) REVERT: D 647 GLN cc_start: 0.7557 (pt0) cc_final: 0.7180 (pt0) REVERT: D 652 VAL cc_start: 0.8307 (m) cc_final: 0.8085 (p) REVERT: D 683 ASP cc_start: 0.7772 (t0) cc_final: 0.7447 (t0) REVERT: D 688 ASN cc_start: 0.8019 (m110) cc_final: 0.7788 (m110) REVERT: D 695 ASP cc_start: 0.6741 (p0) cc_final: 0.6472 (p0) REVERT: D 728 ASN cc_start: 0.7435 (t0) cc_final: 0.7064 (t0) REVERT: D 756 THR cc_start: 0.8672 (m) cc_final: 0.8303 (p) REVERT: D 784 ASN cc_start: 0.8048 (m-40) cc_final: 0.7366 (t0) REVERT: D 786 GLN cc_start: 0.7364 (mt0) cc_final: 0.7028 (mt0) REVERT: F 4 THR cc_start: 0.8517 (m) cc_final: 0.8168 (p) REVERT: F 64 LYS cc_start: 0.8435 (mttm) cc_final: 0.8193 (mmtp) REVERT: F 65 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8647 (p) REVERT: F 123 ASN cc_start: 0.7867 (t0) cc_final: 0.7327 (t0) REVERT: C 55 PHE cc_start: 0.8200 (p90) cc_final: 0.7969 (p90) REVERT: C 57 MET cc_start: 0.6447 (mmm) cc_final: 0.6192 (mmm) REVERT: C 75 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 151 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8244 (p) REVERT: H 37 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6851 (t0) REVERT: H 167 ASP cc_start: 0.7316 (t0) cc_final: 0.7025 (t0) REVERT: H 186 TYR cc_start: 0.7693 (p90) cc_final: 0.7286 (p90) REVERT: H 191 GLN cc_start: 0.8820 (pt0) cc_final: 0.8457 (pt0) outliers start: 49 outliers final: 40 residues processed: 303 average time/residue: 0.2133 time to fit residues: 92.5615 Evaluate side-chains 328 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 240 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 355 LEU 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 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 685 LYS 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 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 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 62 GLU 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 172 LEU 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 Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3592 r_free = 0.3592 target = 0.130138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104442 restraints weight = 17716.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107787 restraints weight = 9861.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109897 restraints weight = 6329.290| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9527 Z= 0.212 Angle : 0.642 8.753 13089 Z= 0.335 Chirality : 0.047 0.189 1569 Planarity : 0.004 0.068 1758 Dihedral : 4.219 18.718 1519 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 7.73 % Allowed : 34.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1424 helix: -1.59 (0.79), residues: 44 sheet: 0.57 (0.21), residues: 620 loop : -0.70 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 204 HIS 0.008 0.002 HIS D 659 PHE 0.024 0.003 PHE D 350 TYR 0.021 0.002 TYR D 331 ARG 0.005 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 419) hydrogen bonds : angle 5.50772 ( 1083) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.70111 ( 10) covalent geometry : bond 0.00447 ( 9522) covalent geometry : angle 0.64167 (13079) *********************** 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 345 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7890 (m-10) cc_final: 0.7615 (m-10) REVERT: D 210 ILE cc_start: 0.8824 (mm) cc_final: 0.8566 (mm) REVERT: D 213 ARG cc_start: 0.7941 (tpp-160) cc_final: 0.7740 (tpp80) REVERT: D 259 ILE cc_start: 0.7907 (mm) cc_final: 0.7559 (mm) REVERT: D 295 ASN cc_start: 0.8218 (p0) cc_final: 0.7949 (p0) REVERT: D 322 LEU cc_start: 0.8690 (tp) cc_final: 0.8457 (tp) REVERT: D 323 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7335 (mm) REVERT: D 324 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6505 (mm110) REVERT: D 346 GLU cc_start: 0.7479 (mp0) cc_final: 0.7227 (mp0) REVERT: D 379 ASN cc_start: 0.7873 (t0) cc_final: 0.7392 (t0) REVERT: D 382 ILE cc_start: 0.8299 (mp) cc_final: 0.7946 (mm) REVERT: D 386 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6910 (mtp) REVERT: D 489 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8043 (p) REVERT: D 494 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7265 (tpp-160) REVERT: D 503 SER cc_start: 0.8631 (m) cc_final: 0.8215 (p) REVERT: D 518 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 532 LEU cc_start: 0.8651 (tp) cc_final: 0.8433 (tp) REVERT: D 537 THR cc_start: 0.8036 (m) cc_final: 0.7709 (p) REVERT: D 557 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7914 (m-10) REVERT: D 588 ASN cc_start: 0.8041 (m-40) cc_final: 0.7564 (m-40) REVERT: D 599 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7904 (t0) REVERT: D 608 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7451 (p) REVERT: D 647 GLN cc_start: 0.7510 (pt0) cc_final: 0.7056 (pt0) REVERT: D 652 VAL cc_start: 0.8332 (m) cc_final: 0.8097 (p) REVERT: D 683 ASP cc_start: 0.7855 (t0) cc_final: 0.7530 (t0) REVERT: D 695 ASP cc_start: 0.6804 (p0) cc_final: 0.6518 (p0) REVERT: D 728 ASN cc_start: 0.7480 (t0) cc_final: 0.7112 (t0) REVERT: D 733 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7702 (p) REVERT: D 756 THR cc_start: 0.8634 (m) cc_final: 0.8079 (p) REVERT: D 784 ASN cc_start: 0.8040 (m-40) cc_final: 0.7414 (t0) REVERT: D 786 GLN cc_start: 0.7332 (mt0) cc_final: 0.6998 (mt0) REVERT: F 4 THR cc_start: 0.8530 (m) cc_final: 0.8184 (p) REVERT: F 65 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8690 (p) REVERT: F 123 ASN cc_start: 0.7939 (t0) cc_final: 0.7433 (t0) REVERT: C 105 LEU cc_start: 0.8455 (mt) cc_final: 0.8251 (mt) REVERT: C 151 THR cc_start: 0.8663 (m) cc_final: 0.8226 (p) REVERT: H 37 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6922 (t0) REVERT: H 167 ASP cc_start: 0.7306 (t0) cc_final: 0.7028 (t0) REVERT: H 186 TYR cc_start: 0.7736 (p90) cc_final: 0.7344 (p90) REVERT: H 191 GLN cc_start: 0.8807 (pt0) cc_final: 0.8471 (pt0) outliers start: 53 outliers final: 40 residues processed: 311 average time/residue: 0.1873 time to fit residues: 83.6096 Evaluate side-chains 339 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 290 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 396 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 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 599 ASP Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 685 LYS 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 733 VAL 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 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 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 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR 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 Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 115 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3629 r_free = 0.3629 target = 0.133011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108719 restraints weight = 17312.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111951 restraints weight = 9677.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114109 restraints weight = 6212.988| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 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 = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9527 Z= 0.127 Angle : 0.629 9.021 13089 Z= 0.319 Chirality : 0.046 0.173 1569 Planarity : 0.004 0.063 1758 Dihedral : 3.913 18.144 1519 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.41 % Allowed : 36.15 % Favored : 57.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1424 helix: -1.46 (0.81), residues: 44 sheet: 0.70 (0.21), residues: 620 loop : -0.65 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 204 HIS 0.007 0.001 HIS D 659 PHE 0.014 0.001 PHE D 380 TYR 0.018 0.001 TYR D 436 ARG 0.004 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 419) hydrogen bonds : angle 5.24201 ( 1083) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.60793 ( 10) covalent geometry : bond 0.00279 ( 9522) covalent geometry : angle 0.62889 (13079) *********************** 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 330 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: D 210 ILE cc_start: 0.8814 (mm) cc_final: 0.8549 (mm) REVERT: D 259 ILE cc_start: 0.7882 (mm) cc_final: 0.6370 (pt) REVERT: D 295 ASN cc_start: 0.8168 (p0) cc_final: 0.7921 (p0) REVERT: D 312 ILE cc_start: 0.8633 (mp) cc_final: 0.8398 (mp) REVERT: D 323 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7055 (mm) REVERT: D 324 GLN cc_start: 0.6652 (mm-40) cc_final: 0.6368 (mm110) REVERT: D 379 ASN cc_start: 0.7994 (t0) cc_final: 0.7563 (t0) REVERT: D 489 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8020 (p) REVERT: D 494 ARG cc_start: 0.7414 (tpp-160) cc_final: 0.7177 (tpp-160) REVERT: D 497 THR cc_start: 0.8222 (m) cc_final: 0.7980 (m) REVERT: D 503 SER cc_start: 0.8597 (m) cc_final: 0.8172 (p) REVERT: D 518 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 532 LEU cc_start: 0.8633 (tp) cc_final: 0.8429 (tp) REVERT: D 537 THR cc_start: 0.8047 (m) cc_final: 0.7711 (p) REVERT: D 588 ASN cc_start: 0.8075 (m-40) cc_final: 0.7613 (m-40) REVERT: D 599 ASP cc_start: 0.8086 (t70) cc_final: 0.7821 (t0) REVERT: D 600 ASN cc_start: 0.8416 (m-40) cc_final: 0.8176 (m-40) REVERT: D 608 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7433 (p) REVERT: D 647 GLN cc_start: 0.7453 (pt0) cc_final: 0.7009 (pt0) REVERT: D 652 VAL cc_start: 0.8315 (m) cc_final: 0.8083 (p) REVERT: D 683 ASP cc_start: 0.7737 (t0) cc_final: 0.7444 (t0) REVERT: D 695 ASP cc_start: 0.6711 (p0) cc_final: 0.6395 (p0) REVERT: D 728 ASN cc_start: 0.7464 (t0) cc_final: 0.7078 (t0) REVERT: D 733 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7569 (p) REVERT: D 756 THR cc_start: 0.8640 (m) cc_final: 0.8309 (p) REVERT: D 784 ASN cc_start: 0.8008 (m-40) cc_final: 0.7427 (t0) REVERT: D 786 GLN cc_start: 0.7206 (mt0) cc_final: 0.6900 (mt0) REVERT: F 4 THR cc_start: 0.8515 (m) cc_final: 0.8175 (p) REVERT: F 123 ASN cc_start: 0.7805 (t0) cc_final: 0.7295 (t0) REVERT: C 55 PHE cc_start: 0.8104 (p90) cc_final: 0.7825 (p90) REVERT: C 151 THR cc_start: 0.8677 (m) cc_final: 0.8304 (p) REVERT: H 37 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6924 (t0) REVERT: H 167 ASP cc_start: 0.7171 (t0) cc_final: 0.6906 (t0) REVERT: H 186 TYR cc_start: 0.7652 (p90) cc_final: 0.7281 (p90) REVERT: H 191 GLN cc_start: 0.8781 (pt0) cc_final: 0.8435 (pt0) outliers start: 44 outliers final: 37 residues processed: 303 average time/residue: 0.1947 time to fit residues: 84.6953 Evaluate side-chains 327 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE 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 338 TYR 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 685 LYS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 733 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 C residue 11 TYR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 104 GLN 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 172 LEU 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 Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105060 restraints weight = 17158.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108249 restraints weight = 9562.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110402 restraints weight = 6120.351| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9527 Z= 0.226 Angle : 0.683 8.737 13089 Z= 0.353 Chirality : 0.047 0.198 1569 Planarity : 0.004 0.062 1758 Dihedral : 4.320 18.815 1519 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 7.58 % Allowed : 35.28 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1424 helix: -1.67 (0.79), residues: 44 sheet: 0.53 (0.20), residues: 626 loop : -0.79 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 36 HIS 0.008 0.002 HIS D 659 PHE 0.028 0.003 PHE D 416 TYR 0.021 0.002 TYR D 338 ARG 0.005 0.001 ARG H 258 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 419) hydrogen bonds : angle 5.54636 ( 1083) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.71141 ( 10) covalent geometry : bond 0.00480 ( 9522) covalent geometry : angle 0.68296 (13079) *********************** 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 345 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: D 210 ILE cc_start: 0.8821 (mm) cc_final: 0.8574 (mm) REVERT: D 259 ILE cc_start: 0.7973 (mm) cc_final: 0.7632 (mm) REVERT: D 295 ASN cc_start: 0.8178 (p0) cc_final: 0.7900 (p0) REVERT: D 323 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7256 (mm) REVERT: D 344 GLN cc_start: 0.8190 (pm20) cc_final: 0.7927 (pt0) REVERT: D 359 LEU cc_start: 0.7621 (mm) cc_final: 0.7346 (mt) REVERT: D 379 ASN cc_start: 0.7842 (t0) cc_final: 0.7363 (t0) REVERT: D 382 ILE cc_start: 0.8327 (mp) cc_final: 0.8018 (mm) REVERT: D 489 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (p) REVERT: D 494 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.7318 (tpp-160) REVERT: D 503 SER cc_start: 0.8631 (m) cc_final: 0.8209 (p) REVERT: D 518 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 532 LEU cc_start: 0.8679 (tp) cc_final: 0.8464 (tp) REVERT: D 537 THR cc_start: 0.8040 (m) cc_final: 0.7765 (p) REVERT: D 547 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8042 (mp10) REVERT: D 557 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: D 588 ASN cc_start: 0.7997 (m-40) cc_final: 0.7550 (m-40) REVERT: D 599 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7819 (t0) REVERT: D 600 ASN cc_start: 0.8410 (m-40) cc_final: 0.7712 (m-40) REVERT: D 608 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7480 (p) REVERT: D 647 GLN cc_start: 0.7493 (pt0) cc_final: 0.7056 (pt0) REVERT: D 652 VAL cc_start: 0.8341 (m) cc_final: 0.8094 (p) REVERT: D 683 ASP cc_start: 0.7855 (t0) cc_final: 0.7535 (t0) REVERT: D 695 ASP cc_start: 0.6790 (p0) cc_final: 0.6502 (p0) REVERT: D 728 ASN cc_start: 0.7468 (t0) cc_final: 0.7103 (t0) REVERT: D 733 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7646 (p) REVERT: D 756 THR cc_start: 0.8639 (m) cc_final: 0.8091 (p) REVERT: D 784 ASN cc_start: 0.8049 (m-40) cc_final: 0.7505 (t0) REVERT: D 786 GLN cc_start: 0.7426 (mt0) cc_final: 0.7126 (mt0) REVERT: F 4 THR cc_start: 0.8517 (m) cc_final: 0.8169 (p) REVERT: F 65 VAL cc_start: 0.9068 (t) cc_final: 0.8645 (p) REVERT: F 123 ASN cc_start: 0.7992 (t0) cc_final: 0.7476 (t0) REVERT: C 55 PHE cc_start: 0.8170 (p90) cc_final: 0.7922 (p90) REVERT: C 77 GLN cc_start: 0.8812 (mm110) cc_final: 0.8465 (mm-40) REVERT: C 105 LEU cc_start: 0.8541 (mt) cc_final: 0.8334 (mt) REVERT: C 151 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8238 (p) REVERT: H 37 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6907 (t0) REVERT: H 167 ASP cc_start: 0.7224 (t0) cc_final: 0.6936 (t0) REVERT: H 186 TYR cc_start: 0.7707 (p90) cc_final: 0.7341 (p90) REVERT: H 191 GLN cc_start: 0.8789 (pt0) cc_final: 0.8494 (pt0) outliers start: 52 outliers final: 38 residues processed: 315 average time/residue: 0.1839 time to fit residues: 83.1166 Evaluate side-chains 332 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE 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 338 TYR 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 599 ASP Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 733 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 C residue 11 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 104 GLN 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 164 SER Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 184 THR 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 Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106015 restraints weight = 17615.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109409 restraints weight = 9898.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111669 restraints weight = 6379.809| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9527 Z= 0.158 Angle : 0.671 14.074 13089 Z= 0.340 Chirality : 0.046 0.180 1569 Planarity : 0.004 0.060 1758 Dihedral : 4.139 19.804 1519 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.14 % Allowed : 36.15 % Favored : 56.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1424 helix: -1.61 (0.80), residues: 44 sheet: 0.57 (0.20), residues: 626 loop : -0.74 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 198 HIS 0.008 0.001 HIS D 659 PHE 0.024 0.002 PHE D 4 TYR 0.022 0.002 TYR D 366 ARG 0.005 0.001 ARG H 258 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 419) hydrogen bonds : angle 5.36726 ( 1083) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.62427 ( 10) covalent geometry : bond 0.00345 ( 9522) covalent geometry : angle 0.67138 (13079) ********************** 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 328 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 1.348 Fit side-chains REVERT: D 205 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8141 (pp) REVERT: D 210 ILE cc_start: 0.8806 (mm) cc_final: 0.8575 (mm) REVERT: D 259 ILE cc_start: 0.7995 (mm) cc_final: 0.7774 (mm) REVERT: D 295 ASN cc_start: 0.8182 (p0) cc_final: 0.7892 (p0) REVERT: D 312 ILE cc_start: 0.8625 (mp) cc_final: 0.8376 (mp) REVERT: D 374 ARG cc_start: 0.7865 (ttm110) cc_final: 0.7568 (ttm110) REVERT: D 379 ASN cc_start: 0.7975 (t0) cc_final: 0.7418 (t0) REVERT: D 489 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8062 (p) REVERT: D 494 ARG cc_start: 0.7590 (tpp-160) cc_final: 0.7363 (tpp-160) REVERT: D 503 SER cc_start: 0.8602 (m) cc_final: 0.8190 (p) REVERT: D 518 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 532 LEU cc_start: 0.8628 (tp) cc_final: 0.8422 (tp) REVERT: D 537 THR cc_start: 0.8045 (m) cc_final: 0.7773 (p) REVERT: D 557 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: D 588 ASN cc_start: 0.8017 (m-40) cc_final: 0.7562 (m-40) REVERT: D 599 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7801 (t0) REVERT: D 600 ASN cc_start: 0.8428 (m-40) cc_final: 0.7816 (m-40) REVERT: D 608 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7449 (p) REVERT: D 647 GLN cc_start: 0.7509 (pt0) cc_final: 0.7067 (pt0) REVERT: D 652 VAL cc_start: 0.8316 (m) cc_final: 0.8073 (p) REVERT: D 683 ASP cc_start: 0.7844 (t0) cc_final: 0.7516 (t0) REVERT: D 695 ASP cc_start: 0.6809 (p0) cc_final: 0.6467 (p0) REVERT: D 728 ASN cc_start: 0.7387 (t0) cc_final: 0.7021 (t0) REVERT: D 733 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7547 (p) REVERT: D 756 THR cc_start: 0.8626 (m) cc_final: 0.8072 (p) REVERT: D 784 ASN cc_start: 0.7997 (m-40) cc_final: 0.7595 (t0) REVERT: D 786 GLN cc_start: 0.7491 (mt0) cc_final: 0.7188 (mt0) REVERT: F 4 THR cc_start: 0.8504 (m) cc_final: 0.8152 (p) REVERT: F 64 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8049 (mmtm) REVERT: F 65 VAL cc_start: 0.9049 (t) cc_final: 0.8624 (p) REVERT: F 123 ASN cc_start: 0.7863 (t0) cc_final: 0.7335 (t0) REVERT: C 55 PHE cc_start: 0.8108 (p90) cc_final: 0.7717 (p90) REVERT: C 105 LEU cc_start: 0.8544 (mt) cc_final: 0.8315 (mt) REVERT: C 151 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8347 (p) REVERT: H 37 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6970 (t0) REVERT: H 167 ASP cc_start: 0.7194 (t0) cc_final: 0.6934 (t0) REVERT: H 186 TYR cc_start: 0.7730 (p90) cc_final: 0.7317 (p90) REVERT: H 191 GLN cc_start: 0.8805 (pt0) cc_final: 0.8507 (pt0) outliers start: 49 outliers final: 39 residues processed: 300 average time/residue: 0.2056 time to fit residues: 89.7756 Evaluate side-chains 322 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 TYR 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 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 599 ASP Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 685 LYS Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 733 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 C residue 11 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 104 GLN 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 164 SER Chi-restraints excluded: chain H residue 172 LEU 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 Chi-restraints excluded: chain H residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104955 restraints weight = 17496.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108290 restraints weight = 9837.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110515 restraints weight = 6371.811| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9527 Z= 0.199 Angle : 0.687 16.148 13089 Z= 0.349 Chirality : 0.047 0.188 1569 Planarity : 0.004 0.059 1758 Dihedral : 4.289 20.026 1519 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 6.85 % Allowed : 36.59 % Favored : 56.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1424 helix: -1.70 (0.79), residues: 44 sheet: 0.48 (0.20), residues: 626 loop : -0.83 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 204 HIS 0.008 0.001 HIS D 659 PHE 0.026 0.002 PHE D 416 TYR 0.022 0.002 TYR D 366 ARG 0.005 0.001 ARG H 258 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 419) hydrogen bonds : angle 5.50421 ( 1083) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.68118 ( 10) covalent geometry : bond 0.00427 ( 9522) covalent geometry : angle 0.68695 (13079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.87 seconds wall clock time: 62 minutes 53.01 seconds (3773.01 seconds total)