Starting phenix.real_space_refine on Thu Sep 18 09:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.map" model { file = "/net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exs_50048/09_2025/9exs_50048.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 39 5.16 5 C 5136 2.51 5 N 1392 2.21 5 O 1448 1.98 5 H 7675 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15691 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5841 Classifications: {'peptide': 374} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 9849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 9849 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 49, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.16 Number of scatterers: 15691 At special positions: 0 Unit cell: (79.23, 88.404, 131.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 Mg 1 11.99 O 1448 8.00 N 1392 7.00 C 5136 6.00 H 7675 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 368.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 7 sheets defined 46.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 4.178A pdb=" N TYR A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.596A pdb=" N TRP A 63 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 132 through 145 Processing helix chain 'A' and resid 154 through 169 removed outlier: 4.383A pdb=" N PHE A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.655A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 244 through 264 removed outlier: 3.650A pdb=" N ALA A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.904A pdb=" N CYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'B' and resid 6 through 14 removed outlier: 3.538A pdb=" N ASN B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 removed outlier: 3.972A pdb=" N HIS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix removed outlier: 3.500A pdb=" N HIS B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 94 Processing helix chain 'B' and resid 108 through 129 removed outlier: 4.295A pdb=" N GLN B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 170 through 191 removed outlier: 3.825A pdb=" N ARG B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.127A pdb=" N GLU B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 4.256A pdb=" N MET B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 377 Processing helix chain 'B' and resid 391 through 404 removed outlier: 4.131A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 Processing helix chain 'B' and resid 578 through 589 removed outlier: 3.611A pdb=" N ARG B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 618 removed outlier: 4.140A pdb=" N ARG B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 655 through 664 Processing helix chain 'B' and resid 665 through 672 removed outlier: 5.145A pdb=" N HIS B 670 " --> pdb=" O ALA B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 675 No H-bonds generated for 'chain 'B' and resid 673 through 675' Processing helix chain 'B' and resid 676 through 682 removed outlier: 3.896A pdb=" N MET B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 716 through 726 removed outlier: 3.634A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 754 through 764 Processing helix chain 'B' and resid 846 through 856 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.506A pdb=" N VAL A 329 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 99 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU A 131 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 96 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY A 213 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 98 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N GLU A 215 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 27 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG A 202 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU A 25 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLY A 204 " --> pdb=" O PRO A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.847A pdb=" N SER A 54 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 274 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET A 284 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 272 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 286 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 270 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP A 233 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 271 " --> pdb=" O TRP A 233 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A 235 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY A 273 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 237 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ARG A 275 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 239 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.398A pdb=" N HIS B 233 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 257 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 235 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN B 51 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR B 236 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 53 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 99 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER B 202 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 101 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.800A pdb=" N ILE B 27 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA7, first strand: chain 'B' and resid 697 through 698 363 hydrogen bonds defined for protein. 1005 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: 2.89 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 7666 1.13 - 1.30: 1435 1.30 - 1.47: 3200 1.47 - 1.65: 3541 1.65 - 1.82: 69 Bond restraints: 15911 Sorted by residual: bond pdb=" N PHE A 205 " pdb=" H PHE A 205 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CE1 TYR B 629 " pdb=" HE1 TYR B 629 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA A 302 " pdb=" H ALA A 302 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE3 TRP A 304 " pdb=" HE3 TRP A 304 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS B 213 " pdb=" H LYS B 213 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 15906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 24890 2.64 - 5.28: 2944 5.28 - 7.93: 846 7.93 - 10.57: 10 10.57 - 13.21: 9 Bond angle restraints: 28699 Sorted by residual: angle pdb=" N ALA B 804 " pdb=" CA ALA B 804 " pdb=" C ALA B 804 " ideal model delta sigma weight residual 111.28 116.76 -5.48 1.09e+00 8.42e-01 2.52e+01 angle pdb=" CB HIS B 250 " pdb=" CG HIS B 250 " pdb=" CD2 HIS B 250 " ideal model delta sigma weight residual 131.20 124.90 6.30 1.30e+00 5.92e-01 2.35e+01 angle pdb=" CB HIS A 133 " pdb=" CG HIS A 133 " pdb=" CD2 HIS A 133 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS B 311 " pdb=" CG HIS B 311 " pdb=" CD2 HIS B 311 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 angle pdb=" N PRO A 9 " pdb=" CA PRO A 9 " pdb=" CB PRO A 9 " ideal model delta sigma weight residual 103.19 105.81 -2.62 5.60e-01 3.19e+00 2.19e+01 ... (remaining 28694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7004 17.79 - 35.58: 322 35.58 - 53.38: 131 53.38 - 71.17: 89 71.17 - 88.96: 5 Dihedral angle restraints: 7551 sinusoidal: 4002 harmonic: 3549 Sorted by residual: dihedral pdb=" CA LYS B 725 " pdb=" C LYS B 725 " pdb=" N GLU B 726 " pdb=" CA GLU B 726 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA HIS B 828 " pdb=" C HIS B 828 " pdb=" N GLN B 829 " pdb=" CA GLN B 829 " ideal model delta harmonic sigma weight residual 180.00 153.14 26.86 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN B 829 " pdb=" C GLN B 829 " pdb=" N HIS B 830 " pdb=" CA HIS B 830 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 7548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 640 0.064 - 0.127: 390 0.127 - 0.191: 127 0.191 - 0.255: 23 0.255 - 0.318: 3 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA HIS B 250 " pdb=" N HIS B 250 " pdb=" C HIS B 250 " pdb=" CB HIS B 250 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA HIS B 796 " pdb=" N HIS B 796 " pdb=" C HIS B 796 " pdb=" CB HIS B 796 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ASP B 640 " pdb=" N ASP B 640 " pdb=" C ASP B 640 " pdb=" CB ASP B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1180 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.189 2.00e-02 2.50e+03 7.35e-02 2.16e+02 pdb=" CG TRP B 623 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP B 623 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 623 " -0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP B 623 " -0.099 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 623 " 0.071 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 623 " -0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP B 623 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 259 " -0.191 2.00e-02 2.50e+03 6.98e-02 1.95e+02 pdb=" CG TRP A 259 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 259 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 259 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 259 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TRP A 259 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 259 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 259 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 259 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 259 " -0.040 2.00e-02 2.50e+03 pdb=" HD1 TRP A 259 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TRP A 259 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP A 259 " 0.104 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 259 " -0.060 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 259 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP A 259 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 362 " 0.172 2.00e-02 2.50e+03 6.36e-02 1.62e+02 pdb=" CG TRP A 362 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 362 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 362 " -0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP A 362 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 362 " -0.064 2.00e-02 2.50e+03 pdb=" CE3 TRP A 362 " -0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 362 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 362 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 362 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 TRP A 362 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 TRP A 362 " 0.036 2.00e-02 2.50e+03 pdb=" HE3 TRP A 362 " -0.053 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 362 " 0.039 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 362 " 0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP A 362 " 0.076 2.00e-02 2.50e+03 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1116 2.21 - 2.81: 28229 2.81 - 3.40: 42671 3.40 - 4.00: 56163 4.00 - 4.60: 81853 Nonbonded interactions: 210032 Sorted by model distance: nonbonded pdb=" HH TYR B 584 " pdb=" OD2 ASP B 637 " model vdw 1.612 2.450 nonbonded pdb=" OE2 GLU A 25 " pdb=" HG SER A 199 " model vdw 1.613 2.450 nonbonded pdb=" HH TYR B 14 " pdb=" OE1 GLU B 322 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASP B 38 " pdb=" HG1 THR B 40 " model vdw 1.624 2.450 nonbonded pdb=" HG SER A 179 " pdb=" OE1 GLU A 182 " model vdw 1.631 2.450 ... (remaining 210027 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.012 0.042 8236 Z= 0.747 Angle : 1.630 7.827 11191 Z= 1.127 Chirality : 0.085 0.318 1183 Planarity : 0.016 0.137 1462 Dihedral : 12.223 88.961 3030 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.37 % Allowed : 1.22 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 994 helix: -0.33 (0.23), residues: 394 sheet: 0.70 (0.42), residues: 133 loop : 0.60 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 41 TYR 0.133 0.020 TYR A 31 PHE 0.052 0.011 PHE B 7 TRP 0.127 0.024 TRP A 259 HIS 0.009 0.003 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.01230 ( 8236) covalent geometry : angle 1.63017 (11191) hydrogen bonds : bond 0.17643 ( 363) hydrogen bonds : angle 7.25029 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.8966 (m) cc_final: 0.8428 (t) REVERT: B 691 TYR cc_start: 0.8140 (m-80) cc_final: 0.7939 (m-80) outliers start: 3 outliers final: 0 residues processed: 130 average time/residue: 0.2153 time to fit residues: 37.0754 Evaluate side-chains 78 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060856 restraints weight = 66081.251| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.65 r_work: 0.2972 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8236 Z= 0.166 Angle : 0.641 6.028 11191 Z= 0.353 Chirality : 0.044 0.155 1183 Planarity : 0.006 0.045 1462 Dihedral : 5.668 23.405 1112 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.73 % Allowed : 4.75 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 994 helix: 1.09 (0.25), residues: 400 sheet: 0.14 (0.38), residues: 149 loop : 0.80 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.015 0.001 TYR B 691 PHE 0.012 0.001 PHE B 773 TRP 0.020 0.002 TRP A 220 HIS 0.006 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8236) covalent geometry : angle 0.64083 (11191) hydrogen bonds : bond 0.06173 ( 363) hydrogen bonds : angle 5.51693 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9218 (m) cc_final: 0.8926 (t) REVERT: A 51 TYR cc_start: 0.8284 (m-80) cc_final: 0.7888 (m-80) REVERT: B 63 CYS cc_start: 0.7701 (m) cc_final: 0.7423 (p) REVERT: B 743 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: B 791 GLU cc_start: 0.9314 (tt0) cc_final: 0.8967 (pm20) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.1933 time to fit residues: 21.7038 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.078777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058910 restraints weight = 67744.296| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.71 r_work: 0.2928 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8236 Z= 0.211 Angle : 0.574 6.101 11191 Z= 0.310 Chirality : 0.043 0.137 1183 Planarity : 0.005 0.042 1462 Dihedral : 5.070 19.296 1112 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.61 % Allowed : 5.48 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.27), residues: 994 helix: 1.39 (0.25), residues: 407 sheet: -0.05 (0.40), residues: 148 loop : 0.80 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.012 0.001 TYR A 31 PHE 0.016 0.001 PHE B 773 TRP 0.016 0.001 TRP B 309 HIS 0.006 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8236) covalent geometry : angle 0.57401 (11191) hydrogen bonds : bond 0.04922 ( 363) hydrogen bonds : angle 5.19882 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9311 (m) cc_final: 0.8999 (t) REVERT: A 123 TYR cc_start: 0.9031 (t80) cc_final: 0.8594 (t80) REVERT: B 743 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7175 (m-80) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1860 time to fit residues: 18.3777 Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain B residue 749 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058345 restraints weight = 67220.463| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.61 r_work: 0.2916 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8236 Z= 0.202 Angle : 0.544 5.453 11191 Z= 0.289 Chirality : 0.043 0.143 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.721 18.596 1112 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.97 % Allowed : 6.46 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.27), residues: 994 helix: 1.68 (0.25), residues: 407 sheet: -0.16 (0.40), residues: 149 loop : 0.73 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.013 0.001 TYR A 31 PHE 0.014 0.001 PHE B 773 TRP 0.013 0.001 TRP B 309 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8236) covalent geometry : angle 0.54368 (11191) hydrogen bonds : bond 0.04336 ( 363) hydrogen bonds : angle 4.92930 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9375 (m) cc_final: 0.9044 (t) REVERT: A 123 TYR cc_start: 0.9052 (t80) cc_final: 0.8526 (t80) REVERT: A 241 MET cc_start: 0.8886 (mtm) cc_final: 0.8661 (mtm) REVERT: B 661 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8665 (mmm) REVERT: B 743 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7202 (m-80) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1855 time to fit residues: 18.3169 Evaluate side-chains 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057942 restraints weight = 68348.786| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.64 r_work: 0.2908 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8236 Z= 0.190 Angle : 0.527 5.555 11191 Z= 0.278 Chirality : 0.042 0.137 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.542 17.255 1112 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.10 % Allowed : 6.94 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.27), residues: 994 helix: 1.90 (0.25), residues: 406 sheet: -0.23 (0.40), residues: 148 loop : 0.74 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.010 0.001 TYR A 31 PHE 0.013 0.001 PHE B 347 TRP 0.012 0.001 TRP B 309 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8236) covalent geometry : angle 0.52745 (11191) hydrogen bonds : bond 0.04068 ( 363) hydrogen bonds : angle 4.77767 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9362 (m) cc_final: 0.9016 (t) REVERT: A 123 TYR cc_start: 0.9062 (t80) cc_final: 0.8492 (t80) REVERT: B 743 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7214 (m-80) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1641 time to fit residues: 15.9531 Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain B residue 749 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058256 restraints weight = 67717.356| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.64 r_work: 0.2909 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8236 Z= 0.145 Angle : 0.501 5.233 11191 Z= 0.261 Chirality : 0.042 0.159 1183 Planarity : 0.004 0.040 1462 Dihedral : 4.387 18.004 1112 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.85 % Allowed : 7.43 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.27), residues: 994 helix: 2.17 (0.25), residues: 407 sheet: -0.25 (0.40), residues: 148 loop : 0.84 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.010 0.001 TYR B 676 PHE 0.011 0.001 PHE B 347 TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8236) covalent geometry : angle 0.50147 (11191) hydrogen bonds : bond 0.03822 ( 363) hydrogen bonds : angle 4.63155 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9343 (m) cc_final: 0.9009 (t) REVERT: A 102 MET cc_start: 0.9154 (mmp) cc_final: 0.8736 (mmp) REVERT: A 123 TYR cc_start: 0.9060 (t80) cc_final: 0.8502 (t80) REVERT: B 743 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7198 (m-80) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1608 time to fit residues: 17.2174 Evaluate side-chains 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.078136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058788 restraints weight = 67207.664| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.55 r_work: 0.2925 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8236 Z= 0.119 Angle : 0.485 5.138 11191 Z= 0.251 Chirality : 0.042 0.139 1183 Planarity : 0.004 0.040 1462 Dihedral : 4.224 17.994 1112 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.73 % Allowed : 7.92 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.27), residues: 994 helix: 2.26 (0.25), residues: 407 sheet: -0.23 (0.39), residues: 148 loop : 0.93 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.008 0.001 TYR B 616 PHE 0.010 0.001 PHE B 347 TRP 0.011 0.001 TRP B 309 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8236) covalent geometry : angle 0.48507 (11191) hydrogen bonds : bond 0.03598 ( 363) hydrogen bonds : angle 4.50544 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9332 (m) cc_final: 0.9001 (t) REVERT: A 102 MET cc_start: 0.9190 (mmp) cc_final: 0.8943 (mmp) REVERT: A 118 MET cc_start: 0.9090 (mtp) cc_final: 0.8850 (mtp) REVERT: A 123 TYR cc_start: 0.9034 (t80) cc_final: 0.8435 (t80) REVERT: B 87 ASP cc_start: 0.8877 (t0) cc_final: 0.8558 (t70) REVERT: B 743 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: B 791 GLU cc_start: 0.9289 (tt0) cc_final: 0.9048 (pm20) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1507 time to fit residues: 16.1063 Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.059018 restraints weight = 67241.149| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.58 r_work: 0.2933 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8236 Z= 0.107 Angle : 0.477 5.560 11191 Z= 0.244 Chirality : 0.041 0.139 1183 Planarity : 0.004 0.040 1462 Dihedral : 4.109 17.576 1112 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.61 % Allowed : 8.53 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.27), residues: 994 helix: 2.41 (0.25), residues: 408 sheet: -0.19 (0.40), residues: 148 loop : 1.01 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.009 0.001 TYR B 616 PHE 0.010 0.001 PHE B 773 TRP 0.010 0.001 TRP B 309 HIS 0.003 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8236) covalent geometry : angle 0.47727 (11191) hydrogen bonds : bond 0.03423 ( 363) hydrogen bonds : angle 4.41929 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9327 (m) cc_final: 0.9011 (t) REVERT: A 123 TYR cc_start: 0.9004 (t80) cc_final: 0.8406 (t80) REVERT: B 743 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: B 791 GLU cc_start: 0.9289 (tt0) cc_final: 0.9031 (pm20) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1488 time to fit residues: 15.9995 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058473 restraints weight = 67936.031| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.54 r_work: 0.2917 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8236 Z= 0.164 Angle : 0.500 5.579 11191 Z= 0.257 Chirality : 0.041 0.134 1183 Planarity : 0.004 0.040 1462 Dihedral : 4.116 18.163 1112 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.85 % Allowed : 8.65 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.27), residues: 994 helix: 2.44 (0.25), residues: 406 sheet: -0.16 (0.40), residues: 148 loop : 0.93 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.009 0.001 TYR A 31 PHE 0.014 0.001 PHE A 37 TRP 0.010 0.001 TRP B 309 HIS 0.004 0.001 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8236) covalent geometry : angle 0.49979 (11191) hydrogen bonds : bond 0.03474 ( 363) hydrogen bonds : angle 4.49858 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9339 (m) cc_final: 0.9003 (t) REVERT: A 123 TYR cc_start: 0.9034 (t80) cc_final: 0.8414 (t80) REVERT: B 56 MET cc_start: 0.8879 (mmm) cc_final: 0.8542 (mmm) REVERT: B 743 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: B 791 GLU cc_start: 0.9280 (tt0) cc_final: 0.9018 (pm20) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.1416 time to fit residues: 13.9637 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain B residue 823 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.078702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059434 restraints weight = 66994.650| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.55 r_work: 0.2941 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8236 Z= 0.094 Angle : 0.475 5.805 11191 Z= 0.239 Chirality : 0.041 0.140 1183 Planarity : 0.004 0.042 1462 Dihedral : 3.977 17.447 1112 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.37 % Allowed : 9.01 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.27), residues: 994 helix: 2.62 (0.25), residues: 407 sheet: -0.05 (0.40), residues: 149 loop : 1.07 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.010 0.001 TYR B 616 PHE 0.014 0.001 PHE A 37 TRP 0.010 0.001 TRP B 309 HIS 0.004 0.001 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8236) covalent geometry : angle 0.47452 (11191) hydrogen bonds : bond 0.03230 ( 363) hydrogen bonds : angle 4.29623 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue THR 243 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LEU 238 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 593 is missing expected H atoms. Skipping. Residue LYS 702 is missing expected H atoms. Skipping. Residue LYS 703 is missing expected H atoms. Skipping. Residue MET 704 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LYS 767 is missing expected H atoms. Skipping. Residue SER 826 is missing expected H atoms. Skipping. Residue LEU 845 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 SER cc_start: 0.9303 (m) cc_final: 0.8986 (t) REVERT: A 102 MET cc_start: 0.9013 (mmp) cc_final: 0.8777 (mmp) REVERT: A 123 TYR cc_start: 0.9022 (t80) cc_final: 0.8410 (t80) REVERT: B 56 MET cc_start: 0.8857 (mmm) cc_final: 0.8497 (mmm) REVERT: B 743 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: B 791 GLU cc_start: 0.9263 (tt0) cc_final: 0.8996 (pm20) outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 0.1569 time to fit residues: 15.4702 Evaluate side-chains 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 743 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.078833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.059621 restraints weight = 66846.225| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.55 r_work: 0.2950 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8236 Z= 0.105 Angle : 0.467 5.602 11191 Z= 0.236 Chirality : 0.041 0.138 1183 Planarity : 0.004 0.039 1462 Dihedral : 3.859 16.984 1112 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.61 % Allowed : 8.89 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.27), residues: 994 helix: 2.76 (0.26), residues: 407 sheet: -0.00 (0.40), residues: 148 loop : 1.12 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.007 0.001 TYR A 294 PHE 0.015 0.001 PHE A 37 TRP 0.009 0.001 TRP B 309 HIS 0.006 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8236) covalent geometry : angle 0.46735 (11191) hydrogen bonds : bond 0.03100 ( 363) hydrogen bonds : angle 4.21717 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.23 seconds wall clock time: 58 minutes 19.94 seconds (3499.94 seconds total)