Starting phenix.real_space_refine on Thu Jul 2 09:59:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9t_38184/07_2026/8x9t_38184.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 53 5.16 5 C 5285 2.51 5 N 1405 2.21 5 O 1517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1770 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 7, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2468 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 376 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1885 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'YNH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8260 At special positions: 0 Unit cell: (88.4, 118.56, 116.48, 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 53 16.00 O 1517 8.00 N 1405 7.00 C 5285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 448.8 milliseconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 33.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.575A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.651A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.565A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.897A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.768A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 569 through 592 Processing helix chain 'R' and resid 599 through 615 Processing helix chain 'R' and resid 616 through 624 removed outlier: 4.004A pdb=" N SER R 622 " --> pdb=" O LEU R 618 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 629 through 662 Processing helix chain 'R' and resid 671 through 679 Processing helix chain 'R' and resid 681 through 693 Processing helix chain 'R' and resid 713 through 721 Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 725 through 744 removed outlier: 4.027A pdb=" N GLY R 729 " --> pdb=" O VAL R 725 " (cutoff:3.500A) Processing helix chain 'R' and resid 754 through 769 Proline residue: R 767 - end of helix Processing helix chain 'R' and resid 787 through 807 removed outlier: 6.315A pdb=" N THR R 793 " --> pdb=" O TYR R 789 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY R 799 " --> pdb=" O ASN R 795 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE R 802 " --> pdb=" O GLN R 798 " (cutoff:3.500A) Processing helix chain 'R' and resid 812 through 827 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.035A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210 removed outlier: 6.373A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.280A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.808A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.253A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.673A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.617A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.036A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.649A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.524A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.925A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.726A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1309 1.31 - 1.43: 2401 1.43 - 1.56: 4656 1.56 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8442 Sorted by residual: bond pdb=" C30 YNH R 901 " pdb=" N27 YNH R 901 " ideal model delta sigma weight residual 1.509 1.307 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C26 YNH R 901 " pdb=" N27 YNH R 901 " ideal model delta sigma weight residual 1.499 1.311 0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C28 YNH R 901 " pdb=" N27 YNH R 901 " ideal model delta sigma weight residual 1.499 1.319 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C17 YNH R 901 " pdb=" C18 YNH R 901 " ideal model delta sigma weight residual 1.389 1.524 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C15 YNH R 901 " pdb=" C16 YNH R 901 " ideal model delta sigma weight residual 1.397 1.528 -0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 8437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 11384 2.61 - 5.23: 94 5.23 - 7.84: 13 7.84 - 10.46: 5 10.46 - 13.07: 1 Bond angle restraints: 11497 Sorted by residual: angle pdb=" N VAL R 725 " pdb=" CA VAL R 725 " pdb=" C VAL R 725 " ideal model delta sigma weight residual 113.47 107.29 6.18 1.01e+00 9.80e-01 3.74e+01 angle pdb=" N ILE R 597 " pdb=" CA ILE R 597 " pdb=" C ILE R 597 " ideal model delta sigma weight residual 111.91 107.41 4.50 8.90e-01 1.26e+00 2.55e+01 angle pdb=" N VAL R 777 " pdb=" CA VAL R 777 " pdb=" C VAL R 777 " ideal model delta sigma weight residual 113.07 107.71 5.36 1.36e+00 5.41e-01 1.55e+01 angle pdb=" CA LEU R 706 " pdb=" CB LEU R 706 " pdb=" CG LEU R 706 " ideal model delta sigma weight residual 116.30 129.37 -13.07 3.50e+00 8.16e-02 1.39e+01 angle pdb=" CB MET R 695 " pdb=" CG MET R 695 " pdb=" SD MET R 695 " ideal model delta sigma weight residual 112.70 122.77 -10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 11492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4195 17.56 - 35.12: 522 35.12 - 52.69: 162 52.69 - 70.25: 34 70.25 - 87.81: 10 Dihedral angle restraints: 4923 sinusoidal: 1725 harmonic: 3198 Sorted by residual: dihedral pdb=" CA TRP R 680 " pdb=" C TRP R 680 " pdb=" N GLY R 681 " pdb=" CA GLY R 681 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual -86.00 -126.00 40.00 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 997 0.042 - 0.084: 269 0.084 - 0.126: 68 0.126 - 0.168: 5 0.168 - 0.211: 1 Chirality restraints: 1340 Sorted by residual: chirality pdb=" CB ILE R 688 " pdb=" CA ILE R 688 " pdb=" CG1 ILE R 688 " pdb=" CG2 ILE R 688 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1337 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.064 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO B 236 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 766 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO R 767 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 767 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 767 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 799 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C GLY R 799 " 0.036 2.00e-02 2.50e+03 pdb=" O GLY R 799 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU R 800 " -0.012 2.00e-02 2.50e+03 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1067 2.75 - 3.29: 8134 3.29 - 3.83: 14636 3.83 - 4.36: 17170 4.36 - 4.90: 29521 Nonbonded interactions: 70528 Sorted by model distance: nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 246 " model vdw 2.213 3.040 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP S 211 " pdb=" OH TYR S 215 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.256 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.257 3.040 ... (remaining 70523 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.006 0.202 8444 Z= 0.316 Angle : 0.633 13.072 11501 Z= 0.341 Chirality : 0.041 0.211 1340 Planarity : 0.005 0.096 1447 Dihedral : 17.745 87.811 2853 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 1.79 % Allowed : 34.57 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 1087 helix: 1.01 (0.29), residues: 357 sheet: -0.06 (0.30), residues: 288 loop : -0.55 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 48 TYR 0.011 0.001 TYR R 602 PHE 0.013 0.001 PHE S 227 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.32 ( 8442) covalent geometry : angle 0.63328 / 0.34 (11497) SS BOND : bond 0.00144 / 0.07 ( 2) SS BOND : angle 0.49731 / 0.24 ( 4) hydrogen bonds : bond 0.14333 / 9.07 ( 396) hydrogen bonds : angle 6.31391 / 4.41 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.232 Fit side-chains REVERT: A 348 ILE cc_start: 0.8716 (mt) cc_final: 0.8440 (mt) REVERT: B 234 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (t80) REVERT: B 245 SER cc_start: 0.8295 (t) cc_final: 0.8032 (t) REVERT: R 620 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7500 (mm) REVERT: S 43 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8297 (mmmm) outliers start: 15 outliers final: 9 residues processed: 212 average time/residue: 0.4623 time to fit residues: 105.0328 Evaluate side-chains 200 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 620 LEU Chi-restraints excluded: chain R residue 739 SER Chi-restraints excluded: chain R residue 742 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 239 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 607 ASN ** R 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115161 restraints weight = 12570.474| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.77 r_work: 0.3412 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8444 Z= 0.136 Angle : 0.529 8.410 11501 Z= 0.281 Chirality : 0.040 0.158 1340 Planarity : 0.004 0.064 1447 Dihedral : 7.218 74.188 1226 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 5.38 % Allowed : 30.02 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1087 helix: 1.38 (0.29), residues: 358 sheet: -0.00 (0.30), residues: 282 loop : -0.50 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.008 0.001 TYR R 602 PHE 0.012 0.001 PHE B 235 TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8442) covalent geometry : angle 0.52929 / 0.28 (11497) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.44792 / 0.15 ( 4) hydrogen bonds : bond 0.03838 / 2.53 ( 396) hydrogen bonds : angle 4.75229 / 3.31 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.312 Fit side-chains REVERT: A 342 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7977 (ttt-90) REVERT: A 348 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 378 ASP cc_start: 0.8000 (m-30) cc_final: 0.7722 (m-30) REVERT: B 59 TYR cc_start: 0.8009 (m-80) cc_final: 0.7562 (m-80) REVERT: B 227 SER cc_start: 0.8690 (t) cc_final: 0.8484 (t) REVERT: S 18 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7975 (ttm110) outliers start: 45 outliers final: 22 residues processed: 220 average time/residue: 0.3586 time to fit residues: 85.7289 Evaluate side-chains 205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 690 SER Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107331 restraints weight = 12317.433| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.70 r_work: 0.3386 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8444 Z= 0.193 Angle : 0.562 8.906 11501 Z= 0.296 Chirality : 0.042 0.150 1340 Planarity : 0.004 0.057 1447 Dihedral : 6.322 57.373 1213 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 4.55 % Allowed : 29.55 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1087 helix: 1.32 (0.28), residues: 358 sheet: -0.09 (0.30), residues: 282 loop : -0.57 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.011 0.001 TYR R 602 PHE 0.016 0.001 PHE B 235 TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8442) covalent geometry : angle 0.56235 / 0.30 (11497) SS BOND : bond 0.00192 / 0.09 ( 2) SS BOND : angle 0.44922 / 0.18 ( 4) hydrogen bonds : bond 0.03924 / 2.60 ( 396) hydrogen bonds : angle 4.73543 / 3.30 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.353 Fit side-chains REVERT: A 214 VAL cc_start: 0.7620 (p) cc_final: 0.7329 (m) REVERT: A 347 ARG cc_start: 0.8178 (ptp90) cc_final: 0.7854 (ttp-110) REVERT: A 378 ASP cc_start: 0.8032 (m-30) cc_final: 0.7780 (m-30) REVERT: A 380 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7772 (ptm-80) REVERT: B 59 TYR cc_start: 0.8148 (m-80) cc_final: 0.7634 (m-80) REVERT: B 227 SER cc_start: 0.8689 (t) cc_final: 0.8452 (t) REVERT: B 246 ASP cc_start: 0.8146 (p0) cc_final: 0.7914 (p0) REVERT: B 318 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7958 (pt) REVERT: R 635 MET cc_start: 0.8240 (ttm) cc_final: 0.8015 (ttm) REVERT: S 18 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8120 (ttm110) outliers start: 38 outliers final: 22 residues processed: 210 average time/residue: 0.3810 time to fit residues: 86.9786 Evaluate side-chains 212 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 634 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 357 HIS B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107829 restraints weight = 12675.607| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.74 r_work: 0.3388 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8444 Z= 0.167 Angle : 0.551 8.276 11501 Z= 0.288 Chirality : 0.041 0.147 1340 Planarity : 0.004 0.052 1447 Dihedral : 6.028 57.366 1209 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 4.90 % Allowed : 29.19 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1087 helix: 1.29 (0.28), residues: 362 sheet: -0.08 (0.30), residues: 280 loop : -0.60 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.010 0.001 TYR R 602 PHE 0.013 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 8442) covalent geometry : angle 0.55108 / 0.29 (11497) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.44368 / 0.18 ( 4) hydrogen bonds : bond 0.03725 / 2.48 ( 396) hydrogen bonds : angle 4.63522 / 3.22 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.310 Fit side-chains REVERT: A 347 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7811 (ttp-110) REVERT: A 348 ILE cc_start: 0.8709 (mt) cc_final: 0.8441 (mt) REVERT: A 378 ASP cc_start: 0.8080 (m-30) cc_final: 0.7835 (m-30) REVERT: A 380 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (ptm-80) REVERT: B 59 TYR cc_start: 0.8178 (m-80) cc_final: 0.7662 (m-80) REVERT: B 227 SER cc_start: 0.8699 (t) cc_final: 0.8386 (t) REVERT: B 246 ASP cc_start: 0.8024 (p0) cc_final: 0.7790 (p0) REVERT: B 318 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8006 (pt) REVERT: S 18 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8110 (ttm110) outliers start: 41 outliers final: 24 residues processed: 215 average time/residue: 0.3580 time to fit residues: 83.7409 Evaluate side-chains 199 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 661 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 86 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 806 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108000 restraints weight = 12556.738| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.73 r_work: 0.3388 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8444 Z= 0.168 Angle : 0.556 9.392 11501 Z= 0.290 Chirality : 0.041 0.137 1340 Planarity : 0.004 0.049 1447 Dihedral : 6.015 58.903 1209 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.38 % Allowed : 29.55 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1087 helix: 1.48 (0.28), residues: 355 sheet: -0.14 (0.30), residues: 280 loop : -0.60 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.011 0.001 TYR R 602 PHE 0.013 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 8442) covalent geometry : angle 0.55559 / 0.29 (11497) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.45289 / 0.18 ( 4) hydrogen bonds : bond 0.03708 / 2.46 ( 396) hydrogen bonds : angle 4.61116 / 3.22 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.310 Fit side-chains REVERT: A 53 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8144 (mtpt) REVERT: A 347 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8011 (ttp-110) REVERT: A 378 ASP cc_start: 0.8111 (m-30) cc_final: 0.7880 (m-30) REVERT: B 59 TYR cc_start: 0.8195 (m-80) cc_final: 0.7685 (m-80) REVERT: B 227 SER cc_start: 0.8686 (t) cc_final: 0.8353 (t) REVERT: B 246 ASP cc_start: 0.7905 (p0) cc_final: 0.7677 (p0) REVERT: B 318 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (pt) REVERT: R 635 MET cc_start: 0.8244 (ttm) cc_final: 0.8033 (ttm) outliers start: 45 outliers final: 29 residues processed: 209 average time/residue: 0.3237 time to fit residues: 74.0043 Evaluate side-chains 204 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 634 VAL Chi-restraints excluded: chain R residue 725 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108445 restraints weight = 12428.115| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.74 r_work: 0.3382 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8444 Z= 0.154 Angle : 0.564 9.346 11501 Z= 0.289 Chirality : 0.041 0.168 1340 Planarity : 0.004 0.047 1447 Dihedral : 5.943 59.098 1209 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.50 % Allowed : 29.19 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1087 helix: 1.38 (0.28), residues: 363 sheet: -0.16 (0.30), residues: 280 loop : -0.59 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 18 TYR 0.011 0.001 TYR R 602 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8442) covalent geometry : angle 0.56366 / 0.29 (11497) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.40896 / 0.15 ( 4) hydrogen bonds : bond 0.03627 / 2.41 ( 396) hydrogen bonds : angle 4.58974 / 3.21 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.191 Fit side-chains REVERT: A 53 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8126 (mtpt) REVERT: A 347 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7909 (ttp-110) REVERT: A 378 ASP cc_start: 0.8104 (m-30) cc_final: 0.7887 (m-30) REVERT: A 380 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7551 (ttt-90) REVERT: B 59 TYR cc_start: 0.8160 (m-80) cc_final: 0.7663 (m-80) REVERT: B 227 SER cc_start: 0.8680 (t) cc_final: 0.8338 (t) REVERT: B 246 ASP cc_start: 0.7891 (p0) cc_final: 0.7674 (p0) REVERT: R 684 LEU cc_start: 0.7954 (tt) cc_final: 0.7743 (tm) REVERT: R 800 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7966 (tp) REVERT: S 18 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8101 (ttm-80) outliers start: 46 outliers final: 31 residues processed: 205 average time/residue: 0.3388 time to fit residues: 76.0134 Evaluate side-chains 203 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 634 VAL Chi-restraints excluded: chain R residue 725 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 774 VAL Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108428 restraints weight = 12497.402| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.74 r_work: 0.3399 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8444 Z= 0.155 Angle : 0.566 9.254 11501 Z= 0.291 Chirality : 0.042 0.158 1340 Planarity : 0.004 0.046 1447 Dihedral : 5.909 59.583 1209 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.14 % Allowed : 30.14 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1087 helix: 1.41 (0.28), residues: 363 sheet: -0.20 (0.30), residues: 280 loop : -0.58 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.011 0.001 TYR R 602 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 8442) covalent geometry : angle 0.56647 / 0.29 (11497) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.43147 / 0.17 ( 4) hydrogen bonds : bond 0.03589 / 2.39 ( 396) hydrogen bonds : angle 4.57887 / 3.22 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.234 Fit side-chains REVERT: A 347 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7990 (ttp-110) REVERT: A 378 ASP cc_start: 0.8134 (m-30) cc_final: 0.7905 (m-30) REVERT: B 59 TYR cc_start: 0.8151 (m-80) cc_final: 0.7610 (m-80) REVERT: B 227 SER cc_start: 0.8673 (t) cc_final: 0.8330 (t) REVERT: B 246 ASP cc_start: 0.7868 (p0) cc_final: 0.7647 (p0) REVERT: B 336 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8235 (mm) outliers start: 43 outliers final: 29 residues processed: 202 average time/residue: 0.3465 time to fit residues: 76.3414 Evaluate side-chains 203 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 634 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 774 VAL Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.0060 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108825 restraints weight = 12442.163| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.74 r_work: 0.3388 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8444 Z= 0.149 Angle : 0.577 9.869 11501 Z= 0.293 Chirality : 0.042 0.160 1340 Planarity : 0.004 0.046 1447 Dihedral : 5.891 59.125 1209 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.43 % Allowed : 30.26 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1087 helix: 1.68 (0.28), residues: 351 sheet: -0.19 (0.30), residues: 281 loop : -0.65 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.013 0.001 TYR A 391 PHE 0.012 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8442) covalent geometry : angle 0.57688 / 0.29 (11497) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.42191 / 0.17 ( 4) hydrogen bonds : bond 0.03578 / 2.37 ( 396) hydrogen bonds : angle 4.55810 / 3.20 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.333 Fit side-chains REVERT: A 347 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7794 (ttp-110) REVERT: A 378 ASP cc_start: 0.8117 (m-30) cc_final: 0.7898 (m-30) REVERT: A 380 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7644 (ttt-90) REVERT: B 59 TYR cc_start: 0.8159 (m-80) cc_final: 0.7606 (m-80) REVERT: B 227 SER cc_start: 0.8683 (t) cc_final: 0.8336 (t) REVERT: B 246 ASP cc_start: 0.7877 (p0) cc_final: 0.7658 (p0) REVERT: B 275 SER cc_start: 0.8236 (p) cc_final: 0.8028 (t) REVERT: R 800 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7953 (tp) outliers start: 37 outliers final: 26 residues processed: 191 average time/residue: 0.3861 time to fit residues: 80.1229 Evaluate side-chains 196 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 634 VAL Chi-restraints excluded: chain R residue 725 VAL Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108889 restraints weight = 12394.967| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.74 r_work: 0.3393 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8444 Z= 0.147 Angle : 0.578 10.844 11501 Z= 0.294 Chirality : 0.042 0.159 1340 Planarity : 0.004 0.046 1447 Dihedral : 5.854 58.933 1209 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.59 % Allowed : 31.58 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1087 helix: 1.54 (0.28), residues: 363 sheet: -0.13 (0.30), residues: 281 loop : -0.59 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.013 0.001 TYR R 602 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8442) covalent geometry : angle 0.57840 / 0.29 (11497) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.50758 / 0.23 ( 4) hydrogen bonds : bond 0.03569 / 2.36 ( 396) hydrogen bonds : angle 4.54233 / 3.18 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.324 Fit side-chains REVERT: A 347 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (ttp-110) REVERT: A 378 ASP cc_start: 0.8104 (m-30) cc_final: 0.7897 (m-30) REVERT: A 380 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7645 (ttt-90) REVERT: B 59 TYR cc_start: 0.8150 (m-80) cc_final: 0.7602 (m-80) REVERT: B 68 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: B 70 LEU cc_start: 0.8343 (tt) cc_final: 0.8020 (tp) REVERT: B 227 SER cc_start: 0.8681 (t) cc_final: 0.8331 (t) REVERT: B 246 ASP cc_start: 0.7885 (p0) cc_final: 0.7659 (p0) REVERT: R 684 LEU cc_start: 0.7913 (tt) cc_final: 0.7694 (tm) REVERT: R 800 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7922 (tp) REVERT: S 18 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7989 (ttm-80) outliers start: 30 outliers final: 25 residues processed: 201 average time/residue: 0.4301 time to fit residues: 93.5094 Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109052 restraints weight = 12345.180| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.73 r_work: 0.3394 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8444 Z= 0.149 Angle : 0.579 11.854 11501 Z= 0.295 Chirality : 0.042 0.158 1340 Planarity : 0.004 0.046 1447 Dihedral : 5.858 58.974 1209 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.47 % Allowed : 31.94 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1087 helix: 1.61 (0.28), residues: 359 sheet: -0.14 (0.30), residues: 281 loop : -0.61 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.012 0.001 TYR R 602 PHE 0.013 0.001 PHE R 817 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8442) covalent geometry : angle 0.57886 / 0.30 (11497) SS BOND : bond 0.00174 / 0.09 ( 2) SS BOND : angle 0.39818 / 0.17 ( 4) hydrogen bonds : bond 0.03553 / 2.35 ( 396) hydrogen bonds : angle 4.54943 / 3.18 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.312 Fit side-chains REVERT: A 347 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (ttp-110) REVERT: A 378 ASP cc_start: 0.8118 (m-30) cc_final: 0.7901 (m-30) REVERT: A 380 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7643 (ttt-90) REVERT: B 31 SER cc_start: 0.8318 (t) cc_final: 0.8045 (m) REVERT: B 59 TYR cc_start: 0.8146 (m-80) cc_final: 0.7610 (m-80) REVERT: B 68 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7964 (ttt-90) REVERT: B 70 LEU cc_start: 0.8360 (tt) cc_final: 0.8057 (tp) REVERT: B 227 SER cc_start: 0.8681 (t) cc_final: 0.8328 (t) REVERT: B 246 ASP cc_start: 0.7876 (p0) cc_final: 0.7648 (p0) REVERT: R 684 LEU cc_start: 0.7909 (tt) cc_final: 0.7703 (tm) outliers start: 29 outliers final: 27 residues processed: 204 average time/residue: 0.4277 time to fit residues: 94.3265 Evaluate side-chains 216 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 800 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109964 restraints weight = 12428.885| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.75 r_work: 0.3423 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8444 Z= 0.123 Angle : 0.568 12.567 11501 Z= 0.288 Chirality : 0.041 0.157 1340 Planarity : 0.004 0.045 1447 Dihedral : 5.773 58.625 1209 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.83 % Allowed : 31.34 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 1087 helix: 1.67 (0.28), residues: 363 sheet: -0.14 (0.30), residues: 283 loop : -0.57 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.011 0.001 TYR R 602 PHE 0.011 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8442) covalent geometry : angle 0.56803 / 0.29 (11497) SS BOND : bond 0.00189 / 0.09 ( 2) SS BOND : angle 0.39220 / 0.15 ( 4) hydrogen bonds : bond 0.03433 / 2.27 ( 396) hydrogen bonds : angle 4.47259 / 3.14 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.14 seconds wall clock time: 49 minutes 47.12 seconds (2987.12 seconds total)