Starting phenix.real_space_refine on Tue Jul 29 22:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.map" model { file = "/net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb0_41144/07_2025/8tb0_41144.cif" } resolution = 3.47 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4039 atoms to isotropic. 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 58 5.16 5 C 5398 2.51 5 N 1447 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8460 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1780 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3756 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 459} Chain breaks: 7 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2539 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 385 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Time building chain proxies: 7.06, per 1000 atoms: 0.83 Number of scatterers: 8460 At special positions: 0 Unit cell: (92.63, 118.59, 129.8, 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 58 16.00 O 1557 8.00 N 1447 7.00 C 5398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 299 " - pdb=" SG CYS R 333 " distance=2.02 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " 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: 2.05 Conformation dependent library (CDL) restraints added in 972.9 milliseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 35.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.684A pdb=" N SER F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.837A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'R' and resid 46 through 68 removed outlier: 3.829A pdb=" N LEU R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL R 63 " --> pdb=" O GLY R 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 75 removed outlier: 4.250A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 92 removed outlier: 3.537A pdb=" N PHE R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 101 removed outlier: 3.707A pdb=" N MET R 98 " --> pdb=" O MET R 94 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 145 removed outlier: 4.092A pdb=" N VAL R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA R 129 " --> pdb=" O PHE R 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL R 138 " --> pdb=" O SER R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 154 removed outlier: 3.970A pdb=" N VAL R 152 " --> pdb=" O MET R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 180 removed outlier: 3.638A pdb=" N VAL R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL R 176 " --> pdb=" O ALA R 172 " (cutoff:3.500A) Proline residue: R 177 - end of helix Processing helix chain 'R' and resid 202 through 237 removed outlier: 4.210A pdb=" N LEU R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE R 208 " --> pdb=" O TYR R 204 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL R 210 " --> pdb=" O GLN R 206 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix removed outlier: 3.780A pdb=" N MET R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE R 232 " --> pdb=" O TYR R 228 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL R 237 " --> pdb=" O ARG R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 313 removed outlier: 3.926A pdb=" N GLN R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU R 301 " --> pdb=" O LEU R 297 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 321 through 331 removed outlier: 3.535A pdb=" N TRP R 328 " --> pdb=" O SER R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 342 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 345 through 353 Processing helix chain 'R' and resid 1470 through 1494 removed outlier: 3.885A pdb=" N GLN R1490 " --> pdb=" O GLN R1486 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL R1491 " --> pdb=" O LYS R1487 " (cutoff:3.500A) Processing helix chain 'R' and resid 1507 through 1512 removed outlier: 3.732A pdb=" N VAL R1512 " --> pdb=" O LYS R1508 " (cutoff:3.500A) Processing helix chain 'R' and resid 1690 through 1694 removed outlier: 3.844A pdb=" N ASN R1694 " --> pdb=" O GLN R1691 " (cutoff:3.500A) Processing helix chain 'R' and resid 1721 through 1733 removed outlier: 3.563A pdb=" N LYS R1726 " --> pdb=" O GLN R1722 " (cutoff:3.500A) Processing helix chain 'R' and resid 1748 through 1759 Processing helix chain 'R' and resid 1763 through 1767 Processing helix chain 'R' and resid 1768 through 1771 removed outlier: 4.000A pdb=" N ALA R1771 " --> pdb=" O PRO R1768 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1768 through 1771' Processing helix chain 'R' and resid 1786 through 1805 removed outlier: 3.853A pdb=" N THR R1790 " --> pdb=" O ASP R1786 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG R1791 " --> pdb=" O PRO R1787 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE R1796 " --> pdb=" O ALA R1792 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG R1797 " --> pdb=" O LYS R1793 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE R1803 " --> pdb=" O GLU R1799 " (cutoff:3.500A) Processing helix chain 'R' and resid 1826 through 1846 removed outlier: 4.348A pdb=" N VAL R1830 " --> pdb=" O ASN R1826 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE R1838 " --> pdb=" O CYS R1834 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR R1846 " --> pdb=" O HIS R1842 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.898A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 4.424A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.679A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AA5, first strand: chain 'F' and resid 128 through 129 removed outlier: 3.625A pdb=" N ARG F 148 " --> pdb=" O THR F 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 135 through 136 removed outlier: 6.636A pdb=" N VAL F 135 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 213 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 1495 through 1496 Processing sheet with id=AA8, first strand: chain 'R' and resid 1500 through 1501 removed outlier: 7.353A pdb=" N LEU R1501 " --> pdb=" O VAL R1702 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE R1699 " --> pdb=" O ILE R1743 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE R1745 " --> pdb=" O ILE R1699 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE R1701 " --> pdb=" O PHE R1745 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.872A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.890A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.423A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.557A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.757A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.468A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2733 1.34 - 1.46: 2020 1.46 - 1.58: 3803 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8640 Sorted by residual: bond pdb=" C PHE R1728 " pdb=" N ASP R1729 " ideal model delta sigma weight residual 1.335 1.318 0.017 1.36e-02 5.41e+03 1.48e+00 bond pdb=" N PRO R1816 " pdb=" CA PRO R1816 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.45e+00 bond pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CA GLY F 193 " pdb=" C GLY F 193 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.26e+00 bond pdb=" CA THR B 50 " pdb=" C THR B 50 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.61e-02 3.86e+03 9.25e-01 ... (remaining 8635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11310 1.50 - 3.00: 336 3.00 - 4.50: 46 4.50 - 6.00: 18 6.00 - 7.50: 7 Bond angle restraints: 11717 Sorted by residual: angle pdb=" N GLU R1470 " pdb=" CA GLU R1470 " pdb=" C GLU R1470 " ideal model delta sigma weight residual 113.43 108.70 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" C TYR R1815 " pdb=" N PRO R1816 " pdb=" CA PRO R1816 " ideal model delta sigma weight residual 119.84 124.08 -4.24 1.25e+00 6.40e-01 1.15e+01 angle pdb=" C ILE B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 121.58 115.57 6.01 1.95e+00 2.63e-01 9.50e+00 angle pdb=" CA ARG B 19 " pdb=" CB ARG B 19 " pdb=" CG ARG B 19 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" CA GLY R1502 " pdb=" C GLY R1502 " pdb=" O GLY R1502 " ideal model delta sigma weight residual 121.88 119.71 2.17 7.80e-01 1.64e+00 7.74e+00 ... (remaining 11712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4537 16.69 - 33.39: 444 33.39 - 50.08: 104 50.08 - 66.78: 11 66.78 - 83.47: 7 Dihedral angle restraints: 5103 sinusoidal: 1947 harmonic: 3156 Sorted by residual: dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -131.07 45.07 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA ALA R1503 " pdb=" C ALA R1503 " pdb=" N GLY R1504 " pdb=" CA GLY R1504 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual 93.00 129.63 -36.63 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 5100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 852 0.036 - 0.072: 363 0.072 - 0.109: 90 0.109 - 0.145: 28 0.145 - 0.181: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA ARG B 19 " pdb=" N ARG B 19 " pdb=" C ARG B 19 " pdb=" CB ARG B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA ILE F 177 " pdb=" N ILE F 177 " pdb=" C ILE F 177 " pdb=" CB ILE F 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CB VAL R 227 " pdb=" CA VAL R 227 " pdb=" CG1 VAL R 227 " pdb=" CG2 VAL R 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1331 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R1780 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R1781 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R1781 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R1781 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 337 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO R 338 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 338 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 338 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 50 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR B 50 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 50 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 51 " 0.009 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.69: 2 1.69 - 2.49: 46 2.49 - 3.29: 9145 3.29 - 4.10: 19606 4.10 - 4.90: 36046 Warning: very small nonbonded interaction distances. Nonbonded interactions: 64845 Sorted by model distance: nonbonded pdb=" CD2 LEU R1500 " pdb=" OE2 GLU R1505 " model vdw 0.884 3.460 nonbonded pdb=" CD2 LEU R1500 " pdb=" CD GLU R1505 " model vdw 1.155 3.690 nonbonded pdb=" CD2 LEU R1500 " pdb=" OE1 GLU R1505 " model vdw 1.862 3.460 nonbonded pdb=" CG LEU R1500 " pdb=" OE2 GLU R1505 " model vdw 1.894 3.470 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.155 3.040 ... (remaining 64840 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: 0.010 Normalize map: mean=0, sd=1: 11.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8645 Z= 0.141 Angle : 0.653 7.495 11727 Z= 0.365 Chirality : 0.043 0.181 1334 Planarity : 0.004 0.059 1483 Dihedral : 14.041 83.472 3052 Min Nonbonded Distance : 0.884 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.82 (0.25), residues: 1066 helix: -0.45 (0.29), residues: 315 sheet: -1.22 (0.37), residues: 215 loop : -1.63 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS F 220 PHE 0.014 0.001 PHE R1728 TYR 0.012 0.001 TYR F 102 ARG 0.011 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.20413 ( 319) hydrogen bonds : angle 6.64485 ( 885) SS BOND : bond 0.00481 ( 5) SS BOND : angle 1.34394 ( 10) covalent geometry : bond 0.00286 ( 8640) covalent geometry : angle 0.65188 (11717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: F 126 ILE cc_start: 0.6829 (mm) cc_final: 0.5912 (mm) REVERT: R 1487 LYS cc_start: 0.7051 (mttp) cc_final: 0.6115 (mtpp) REVERT: R 1511 ILE cc_start: 0.7822 (mm) cc_final: 0.7520 (mm) REVERT: G 46 LYS cc_start: 0.8331 (mtmm) cc_final: 0.8051 (tptt) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2259 time to fit residues: 42.1940 Evaluate side-chains 105 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R1845 GLN B 155 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139037 restraints weight = 10833.289| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.69 r_work: 0.3621 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8645 Z= 0.130 Angle : 0.584 8.020 11727 Z= 0.301 Chirality : 0.043 0.147 1334 Planarity : 0.004 0.047 1483 Dihedral : 4.511 19.565 1183 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.32 % Allowed : 9.37 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.58 (0.25), residues: 1066 helix: -0.11 (0.28), residues: 331 sheet: -1.23 (0.36), residues: 223 loop : -1.54 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE R1795 TYR 0.012 0.001 TYR R 303 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 319) hydrogen bonds : angle 5.18384 ( 885) SS BOND : bond 0.00477 ( 5) SS BOND : angle 1.31256 ( 10) covalent geometry : bond 0.00293 ( 8640) covalent geometry : angle 0.58256 (11717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 1511 ILE cc_start: 0.7624 (mm) cc_final: 0.7387 (mm) REVERT: R 1726 LYS cc_start: 0.7647 (pttp) cc_final: 0.7269 (mmtp) REVERT: R 1769 GLU cc_start: 0.8229 (mp0) cc_final: 0.7910 (mp0) REVERT: B 19 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7884 (ptt-90) REVERT: G 46 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8169 (tptt) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.2401 time to fit residues: 39.7055 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1684 ASP Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136889 restraints weight = 10942.701| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.72 r_work: 0.3594 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8645 Z= 0.132 Angle : 0.561 7.806 11727 Z= 0.288 Chirality : 0.042 0.148 1334 Planarity : 0.004 0.040 1483 Dihedral : 4.417 19.897 1183 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.76 % Allowed : 12.02 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.44 (0.26), residues: 1066 helix: 0.15 (0.29), residues: 326 sheet: -1.26 (0.35), residues: 224 loop : -1.50 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE R 306 TYR 0.010 0.001 TYR F 102 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 319) hydrogen bonds : angle 4.91393 ( 885) SS BOND : bond 0.00468 ( 5) SS BOND : angle 1.30885 ( 10) covalent geometry : bond 0.00305 ( 8640) covalent geometry : angle 0.55954 (11717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: R 1487 LYS cc_start: 0.8056 (mttp) cc_final: 0.7827 (mtpp) REVERT: R 1726 LYS cc_start: 0.7646 (pttp) cc_final: 0.7289 (mmtp) REVERT: R 1769 GLU cc_start: 0.8253 (mp0) cc_final: 0.7981 (mp0) REVERT: B 19 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7798 (ptt-90) REVERT: G 46 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8128 (tptt) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.2304 time to fit residues: 37.2778 Evaluate side-chains 117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1798 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.176481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136069 restraints weight = 10864.924| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.68 r_work: 0.3576 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8645 Z= 0.141 Angle : 0.564 7.828 11727 Z= 0.290 Chirality : 0.043 0.152 1334 Planarity : 0.004 0.037 1483 Dihedral : 4.415 20.254 1183 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.21 % Allowed : 14.55 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.40 (0.26), residues: 1066 helix: 0.25 (0.29), residues: 326 sheet: -1.34 (0.35), residues: 230 loop : -1.46 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.002 PHE R1795 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 319) hydrogen bonds : angle 4.83180 ( 885) SS BOND : bond 0.00448 ( 5) SS BOND : angle 1.36001 ( 10) covalent geometry : bond 0.00329 ( 8640) covalent geometry : angle 0.56250 (11717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 1726 LYS cc_start: 0.7647 (pttp) cc_final: 0.7292 (mmtp) REVERT: G 46 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8141 (tptt) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 0.2228 time to fit residues: 37.7204 Evaluate side-chains 124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 333 CYS Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1798 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134548 restraints weight = 10889.722| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.66 r_work: 0.3563 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8645 Z= 0.168 Angle : 0.597 8.184 11727 Z= 0.309 Chirality : 0.044 0.159 1334 Planarity : 0.004 0.037 1483 Dihedral : 4.568 20.360 1183 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.87 % Allowed : 16.54 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.47 (0.26), residues: 1066 helix: 0.24 (0.29), residues: 326 sheet: -1.46 (0.35), residues: 228 loop : -1.50 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.002 PHE R 306 TYR 0.012 0.002 TYR F 163 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 319) hydrogen bonds : angle 4.90340 ( 885) SS BOND : bond 0.00496 ( 5) SS BOND : angle 1.43033 ( 10) covalent geometry : bond 0.00396 ( 8640) covalent geometry : angle 0.59541 (11717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.950 Fit side-chains REVERT: R 303 TYR cc_start: 0.7561 (t80) cc_final: 0.7275 (t80) REVERT: R 1726 LYS cc_start: 0.7630 (pttp) cc_final: 0.7287 (mmtp) REVERT: B 19 ARG cc_start: 0.8235 (ptt-90) cc_final: 0.7950 (ptt-90) REVERT: G 46 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8152 (tptt) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.2374 time to fit residues: 40.1067 Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 0.0870 chunk 19 optimal weight: 0.0170 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1675 HIS B 155 ASN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.175546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137197 restraints weight = 10720.970| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.30 r_work: 0.3618 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8645 Z= 0.128 Angle : 0.582 9.239 11727 Z= 0.297 Chirality : 0.042 0.151 1334 Planarity : 0.004 0.036 1483 Dihedral : 4.427 22.138 1183 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.09 % Allowed : 17.31 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.34 (0.26), residues: 1066 helix: 0.40 (0.29), residues: 329 sheet: -1.24 (0.36), residues: 221 loop : -1.56 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS B 225 PHE 0.017 0.001 PHE R1667 TYR 0.008 0.001 TYR F 102 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 319) hydrogen bonds : angle 4.79739 ( 885) SS BOND : bond 0.00588 ( 5) SS BOND : angle 3.12050 ( 10) covalent geometry : bond 0.00298 ( 8640) covalent geometry : angle 0.57531 (11717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.881 Fit side-chains REVERT: R 1726 LYS cc_start: 0.7743 (pttp) cc_final: 0.7410 (mmtp) REVERT: B 19 ARG cc_start: 0.8255 (ptt-90) cc_final: 0.7888 (ptt-90) REVERT: B 303 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6668 (p0) REVERT: G 46 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8151 (tptt) outliers start: 28 outliers final: 21 residues processed: 125 average time/residue: 0.2367 time to fit residues: 40.1421 Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1774 THR Chi-restraints excluded: chain R residue 1798 ASP Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137470 restraints weight = 10864.489| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.51 r_work: 0.3578 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8645 Z= 0.134 Angle : 0.588 7.859 11727 Z= 0.300 Chirality : 0.043 0.153 1334 Planarity : 0.003 0.036 1483 Dihedral : 4.415 21.767 1183 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.42 % Allowed : 18.08 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.31 (0.26), residues: 1066 helix: 0.43 (0.29), residues: 330 sheet: -1.33 (0.36), residues: 223 loop : -1.49 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.002 PHE R1795 TYR 0.009 0.001 TYR F 102 ARG 0.006 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 319) hydrogen bonds : angle 4.72639 ( 885) SS BOND : bond 0.00632 ( 5) SS BOND : angle 2.75795 ( 10) covalent geometry : bond 0.00313 ( 8640) covalent geometry : angle 0.58252 (11717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.868 Fit side-chains REVERT: R 303 TYR cc_start: 0.7587 (t80) cc_final: 0.7278 (t80) REVERT: R 1726 LYS cc_start: 0.7655 (pttp) cc_final: 0.7358 (mmtp) REVERT: B 19 ARG cc_start: 0.8244 (ptt-90) cc_final: 0.7975 (ptt-90) REVERT: B 303 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6589 (p0) REVERT: G 46 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8170 (tptt) outliers start: 31 outliers final: 24 residues processed: 129 average time/residue: 0.2959 time to fit residues: 52.4743 Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1774 THR Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136918 restraints weight = 10906.460| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.54 r_work: 0.3569 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8645 Z= 0.140 Angle : 0.592 8.050 11727 Z= 0.303 Chirality : 0.043 0.155 1334 Planarity : 0.004 0.039 1483 Dihedral : 4.432 22.240 1183 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.53 % Allowed : 18.85 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.29 (0.26), residues: 1066 helix: 0.53 (0.29), residues: 328 sheet: -1.38 (0.36), residues: 226 loop : -1.50 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.002 PHE R1667 TYR 0.009 0.001 TYR F 102 ARG 0.008 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 319) hydrogen bonds : angle 4.70088 ( 885) SS BOND : bond 0.00691 ( 5) SS BOND : angle 2.41335 ( 10) covalent geometry : bond 0.00330 ( 8640) covalent geometry : angle 0.58843 (11717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.930 Fit side-chains REVERT: R 303 TYR cc_start: 0.7628 (t80) cc_final: 0.7334 (t80) REVERT: R 1726 LYS cc_start: 0.7660 (pttp) cc_final: 0.7356 (mmtp) REVERT: B 19 ARG cc_start: 0.8266 (ptt-90) cc_final: 0.7942 (ptt-90) REVERT: B 105 TYR cc_start: 0.7971 (t80) cc_final: 0.7743 (t80) REVERT: B 303 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6580 (p0) REVERT: G 46 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8143 (tptt) outliers start: 32 outliers final: 26 residues processed: 131 average time/residue: 0.2253 time to fit residues: 40.4493 Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1774 THR Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137913 restraints weight = 10786.262| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.50 r_work: 0.3587 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8645 Z= 0.130 Angle : 0.588 8.128 11727 Z= 0.300 Chirality : 0.042 0.153 1334 Planarity : 0.004 0.042 1483 Dihedral : 4.368 21.818 1183 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.64 % Allowed : 18.96 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.22 (0.26), residues: 1066 helix: 0.56 (0.29), residues: 329 sheet: -1.29 (0.36), residues: 224 loop : -1.47 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.002 PHE R1795 TYR 0.009 0.001 TYR B 105 ARG 0.008 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 319) hydrogen bonds : angle 4.63292 ( 885) SS BOND : bond 0.00673 ( 5) SS BOND : angle 2.19175 ( 10) covalent geometry : bond 0.00304 ( 8640) covalent geometry : angle 0.58457 (11717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.052 Fit side-chains REVERT: R 303 TYR cc_start: 0.7583 (t80) cc_final: 0.7284 (t80) REVERT: R 1726 LYS cc_start: 0.7643 (pttp) cc_final: 0.7363 (mmtp) REVERT: B 19 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.7966 (ptt-90) REVERT: B 105 TYR cc_start: 0.7928 (t80) cc_final: 0.7678 (t80) REVERT: B 303 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6604 (p0) REVERT: G 46 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8121 (tptt) outliers start: 33 outliers final: 28 residues processed: 133 average time/residue: 0.2807 time to fit residues: 51.1010 Evaluate side-chains 141 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1510 THR Chi-restraints excluded: chain R residue 1705 SER Chi-restraints excluded: chain R residue 1739 ASP Chi-restraints excluded: chain R residue 1774 THR Chi-restraints excluded: chain R residue 1798 ASP Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.0010 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 82 optimal weight: 0.0070 chunk 73 optimal weight: 5.9990 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.181050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141310 restraints weight = 10647.895| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.53 r_work: 0.3647 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8645 Z= 0.104 Angle : 0.568 8.058 11727 Z= 0.288 Chirality : 0.041 0.143 1334 Planarity : 0.003 0.044 1483 Dihedral : 4.131 21.578 1183 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.65 % Allowed : 19.85 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.04 (0.26), residues: 1066 helix: 0.72 (0.30), residues: 325 sheet: -1.17 (0.35), residues: 236 loop : -1.35 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE R1667 TYR 0.013 0.001 TYR F 178 ARG 0.009 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 319) hydrogen bonds : angle 4.44148 ( 885) SS BOND : bond 0.00565 ( 5) SS BOND : angle 1.57996 ( 10) covalent geometry : bond 0.00238 ( 8640) covalent geometry : angle 0.56651 (11717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.882 Fit side-chains REVERT: R 303 TYR cc_start: 0.7418 (t80) cc_final: 0.7081 (t80) REVERT: R 1726 LYS cc_start: 0.7566 (pttp) cc_final: 0.7342 (mmtp) REVERT: B 19 ARG cc_start: 0.8285 (ptt-90) cc_final: 0.8006 (ptt-90) REVERT: B 105 TYR cc_start: 0.7806 (t80) cc_final: 0.7574 (t80) REVERT: B 303 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6549 (p0) REVERT: G 46 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8194 (tptt) REVERT: G 47 GLU cc_start: 0.8480 (mp0) cc_final: 0.8015 (mp0) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.3286 time to fit residues: 60.0310 Evaluate side-chains 130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 150 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 1490 GLN Chi-restraints excluded: chain R residue 1839 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141860 restraints weight = 10827.939| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.71 r_work: 0.3646 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8645 Z= 0.112 Angle : 0.588 9.650 11727 Z= 0.295 Chirality : 0.042 0.161 1334 Planarity : 0.003 0.047 1483 Dihedral : 4.140 21.474 1183 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.43 % Allowed : 20.40 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.96 (0.26), residues: 1066 helix: 0.79 (0.29), residues: 329 sheet: -1.09 (0.36), residues: 231 loop : -1.34 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.024 0.001 PHE R1795 TYR 0.013 0.001 TYR F 178 ARG 0.009 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 319) hydrogen bonds : angle 4.50686 ( 885) SS BOND : bond 0.00697 ( 5) SS BOND : angle 3.11942 ( 10) covalent geometry : bond 0.00265 ( 8640) covalent geometry : angle 0.58092 (11717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.63 seconds wall clock time: 103 minutes 25.14 seconds (6205.14 seconds total)