Starting phenix.real_space_refine on Tue Dec 31 12:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exs_50048/12_2024/9exs_50048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exs_50048/12_2024/9exs_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_50048/12_2024/9exs_50048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exs_50048/12_2024/9exs_50048.map" model { file = "/net/cci-nas-00/data/ceres_data/9exs_50048/12_2024/9exs_50048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exs_50048/12_2024/9exs_50048.cif" } resolution = 3.28 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= 0.010 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5} 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: 7.96, per 1000 atoms: 0.51 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: 4.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.34 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: 6.24 Time building geometry restraints manager: 4.77 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.250 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- 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= 0.807 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 (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: 0.19 (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 TRP 0.127 0.024 TRP A 259 HIS 0.009 0.003 HIS B 389 PHE 0.052 0.011 PHE B 7 TYR 0.133 0.020 TYR A 31 ARG 0.011 0.001 ARG B 41 *********************** 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 : 1.344 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: A 43 SER cc_start: 0.8966 (m) cc_final: 0.8427 (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: 0.4851 time to fit residues: 83.8059 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 : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8236 Z= 0.214 Angle : 0.643 5.962 11191 Z= 0.358 Chirality : 0.045 0.157 1183 Planarity : 0.006 0.050 1462 Dihedral : 5.669 23.260 1112 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.73 % Allowed : 4.99 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.26), residues: 994 helix: 1.06 (0.25), residues: 400 sheet: 0.25 (0.38), residues: 149 loop : 0.83 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 220 HIS 0.007 0.001 HIS B 752 PHE 0.013 0.002 PHE B 773 TYR 0.017 0.002 TYR B 691 ARG 0.003 0.000 ARG A 173 *********************** 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 85 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.187 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: 0.9022 (m) cc_final: 0.8527 (t) REVERT: B 743 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6448 (m-80) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 0.4659 time to fit residues: 53.1318 Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8236 Z= 0.265 Angle : 0.569 6.083 11191 Z= 0.304 Chirality : 0.042 0.138 1183 Planarity : 0.005 0.042 1462 Dihedral : 5.003 19.242 1112 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.49 % Allowed : 5.97 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.27), residues: 994 helix: 1.44 (0.25), residues: 407 sheet: 0.02 (0.41), residues: 147 loop : 0.86 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 309 HIS 0.006 0.001 HIS A 351 PHE 0.016 0.001 PHE B 773 TYR 0.012 0.001 TYR A 31 ARG 0.003 0.000 ARG A 173 *********************** 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: 4 poor density : 70 time to evaluate : 1.286 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: 0.9111 (m) cc_final: 0.8665 (t) REVERT: B 743 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6572 (m-80) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.4537 time to fit residues: 45.1760 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 : 1.295 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8236 Z= 0.166 Angle : 0.509 5.025 11191 Z= 0.266 Chirality : 0.042 0.140 1183 Planarity : 0.004 0.040 1462 Dihedral : 4.602 18.365 1112 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.49 % Allowed : 6.58 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.27), residues: 994 helix: 1.87 (0.25), residues: 406 sheet: 0.10 (0.40), residues: 151 loop : 1.04 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS A 351 PHE 0.012 0.001 PHE B 347 TYR 0.009 0.001 TYR A 31 ARG 0.001 0.000 ARG A 124 *********************** 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 75 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.322 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: 0.9111 (m) cc_final: 0.8662 (t) REVERT: B 661 MET cc_start: 0.7951 (mmm) cc_final: 0.7626 (mmm) REVERT: B 743 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6608 (m-80) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.4753 time to fit residues: 48.2579 Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 743 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8236 Z= 0.349 Angle : 0.552 5.811 11191 Z= 0.293 Chirality : 0.042 0.141 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.576 17.840 1112 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.85 % Allowed : 7.55 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.27), residues: 994 helix: 1.89 (0.25), residues: 405 sheet: -0.13 (0.40), residues: 148 loop : 0.74 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.005 0.001 HIS B 250 PHE 0.015 0.002 PHE B 773 TYR 0.011 0.001 TYR A 31 ARG 0.002 0.000 ARG B 219 *********************** 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 73 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.494 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: 0.9233 (m) cc_final: 0.8722 (t) REVERT: B 743 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6647 (m-80) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.4081 time to fit residues: 41.1006 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8236 Z= 0.151 Angle : 0.497 6.990 11191 Z= 0.256 Chirality : 0.042 0.154 1183 Planarity : 0.004 0.051 1462 Dihedral : 4.341 16.566 1112 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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 (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: 1.88 (0.27), residues: 994 helix: 2.20 (0.25), residues: 407 sheet: -0.12 (0.40), residues: 148 loop : 1.02 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS A 351 PHE 0.010 0.001 PHE B 347 TYR 0.010 0.001 TYR B 616 ARG 0.007 0.000 ARG A 337 *********************** 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 75 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 1.423 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: 0.9180 (m) cc_final: 0.8677 (t) REVERT: B 743 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6692 (m-80) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.3871 time to fit residues: 40.6032 Evaluate side-chains 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 55 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8236 Z= 0.222 Angle : 0.497 5.033 11191 Z= 0.257 Chirality : 0.041 0.138 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.239 17.235 1112 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.61 % Allowed : 8.40 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.27), residues: 994 helix: 2.26 (0.25), residues: 407 sheet: -0.23 (0.39), residues: 148 loop : 1.02 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS A 351 PHE 0.016 0.001 PHE A 37 TYR 0.009 0.001 TYR A 31 ARG 0.007 0.000 ARG A 337 *********************** 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 73 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.286 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: 0.9182 (m) cc_final: 0.8698 (t) REVERT: B 87 ASP cc_start: 0.8012 (t70) cc_final: 0.7731 (t70) REVERT: B 743 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6710 (m-80) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.3941 time to fit residues: 40.8892 Evaluate side-chains 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8236 Z= 0.143 Angle : 0.476 5.593 11191 Z= 0.243 Chirality : 0.041 0.141 1183 Planarity : 0.004 0.043 1462 Dihedral : 4.104 16.875 1112 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.49 % Allowed : 8.77 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.27), residues: 994 helix: 2.47 (0.25), residues: 407 sheet: -0.18 (0.39), residues: 148 loop : 1.12 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 309 HIS 0.003 0.001 HIS A 351 PHE 0.012 0.001 PHE A 37 TYR 0.011 0.001 TYR B 616 ARG 0.006 0.000 ARG A 337 *********************** 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 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.356 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: 0.9155 (m) cc_final: 0.8660 (t) REVERT: B 87 ASP cc_start: 0.8033 (t70) cc_final: 0.7706 (t70) REVERT: B 743 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6651 (m-80) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.3813 time to fit residues: 38.4070 Evaluate side-chains 68 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 743 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8236 Z= 0.202 Angle : 0.485 9.417 11191 Z= 0.248 Chirality : 0.041 0.137 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.063 16.936 1112 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.61 % Allowed : 8.65 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.27), residues: 994 helix: 2.55 (0.25), residues: 407 sheet: -0.14 (0.40), residues: 148 loop : 1.10 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 309 HIS 0.004 0.001 HIS B 677 PHE 0.012 0.001 PHE A 37 TYR 0.008 0.001 TYR A 31 ARG 0.005 0.000 ARG A 337 *********************** 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 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.355 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: 0.9161 (m) cc_final: 0.8666 (t) REVERT: B 87 ASP cc_start: 0.8070 (t70) cc_final: 0.7748 (t70) REVERT: B 743 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6707 (m-80) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.3606 time to fit residues: 34.9605 Evaluate side-chains 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 711 LEU 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 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 8236 Z= 0.197 Angle : 0.482 7.446 11191 Z= 0.246 Chirality : 0.041 0.139 1183 Planarity : 0.004 0.042 1462 Dihedral : 4.016 16.961 1112 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.61 % Allowed : 8.65 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.27), residues: 994 helix: 2.60 (0.25), residues: 407 sheet: -0.16 (0.39), residues: 148 loop : 1.05 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS B 677 PHE 0.012 0.001 PHE A 37 TYR 0.009 0.001 TYR A 31 ARG 0.005 0.000 ARG A 337 ********************** 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: 5 poor density : 63 time to evaluate : 1.333 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: 0.9158 (m) cc_final: 0.8673 (t) REVERT: B 87 ASP cc_start: 0.8026 (t70) cc_final: 0.7690 (t70) REVERT: B 743 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6654 (m-80) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.3687 time to fit residues: 36.1796 Evaluate side-chains 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 711 LEU 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 73 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.079228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059585 restraints weight = 66999.264| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.57 r_work: 0.2948 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4141 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= 0.136 Angle : 0.465 7.616 11191 Z= 0.234 Chirality : 0.041 0.141 1183 Planarity : 0.004 0.043 1462 Dihedral : 3.897 16.716 1112 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.37 % Allowed : 8.89 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.27), residues: 994 helix: 2.74 (0.25), residues: 406 sheet: -0.07 (0.40), residues: 148 loop : 1.14 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 309 HIS 0.004 0.001 HIS B 677 PHE 0.013 0.001 PHE A 37 TYR 0.011 0.001 TYR B 616 ARG 0.005 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3642.42 seconds wall clock time: 66 minutes 14.24 seconds (3974.24 seconds total)