Starting phenix.real_space_refine on Mon Jan 20 19:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exs_50048/01_2025/9exs_50048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exs_50048/01_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_50048/01_2025/9exs_50048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exs_50048/01_2025/9exs_50048.map" model { file = "/net/cci-nas-00/data/ceres_data/9exs_50048/01_2025/9exs_50048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exs_50048/01_2025/9exs_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.46, per 1000 atoms: 0.54 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: 4.29 Conformation dependent library (CDL) restraints added in 1.6 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: 1.41 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: 5.84 Time building geometry restraints manager: 4.97 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: 2.260 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: 0.260 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- 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 : 1.260 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: 0.5016 time to fit residues: 86.1859 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 : 1.351 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.080533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060889 restraints weight = 65769.972| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.65 r_work: 0.2955 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 1.302 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: 0.9224 (m) cc_final: 0.8902 (t) REVERT: B 63 CYS cc_start: 0.7698 (m) cc_final: 0.7439 (p) REVERT: B 743 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: B 791 GLU cc_start: 0.9334 (tt0) cc_final: 0.8969 (pm20) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 0.4702 time to fit residues: 53.1581 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 : 1.373 ------------------------------------------------------------------------------- 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 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.080012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060208 restraints weight = 65980.520| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.66 r_work: 0.2951 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2878 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= 0.215 Angle : 0.555 5.821 11191 Z= 0.297 Chirality : 0.042 0.139 1183 Planarity : 0.005 0.041 1462 Dihedral : 5.000 19.348 1112 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.37 % Allowed : 5.72 % 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 (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: 1.42 (0.27), residues: 994 helix: 1.50 (0.26), residues: 406 sheet: 0.10 (0.41), residues: 147 loop : 0.92 (0.31), residues: 441 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 0.015 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 75 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.255 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: 0.9270 (m) cc_final: 0.8966 (t) REVERT: B 791 GLU cc_start: 0.9340 (tt0) cc_final: 0.8994 (pm20) outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.4625 time to fit residues: 46.7232 Evaluate side-chains 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.077232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057431 restraints weight = 68032.233| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.62 r_work: 0.2894 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8236 Z= 0.426 Angle : 0.603 7.265 11191 Z= 0.326 Chirality : 0.044 0.158 1183 Planarity : 0.005 0.041 1462 Dihedral : 4.873 19.118 1112 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 (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: 1.09 (0.26), residues: 994 helix: 1.48 (0.25), residues: 405 sheet: -0.21 (0.40), residues: 149 loop : 0.52 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 309 HIS 0.007 0.001 HIS B 250 PHE 0.018 0.002 PHE B 254 TYR 0.014 0.002 TYR A 31 ARG 0.002 0.000 ARG A 363 *********************** 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 73 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.491 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: 0.9407 (m) cc_final: 0.9083 (t) REVERT: B 743 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7168 (m-80) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.4307 time to fit residues: 43.5410 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 : 1.225 ------------------------------------------------------------------------------- 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 711 LEU Chi-restraints excluded: chain B residue 743 PHE Chi-restraints excluded: chain B residue 749 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058851 restraints weight = 67653.732| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.64 r_work: 0.2926 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3450 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= 0.169 Angle : 0.509 5.998 11191 Z= 0.266 Chirality : 0.042 0.139 1183 Planarity : 0.004 0.043 1462 Dihedral : 4.556 18.412 1112 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.73 % Allowed : 7.31 % 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 (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: 1.61 (0.27), residues: 994 helix: 1.94 (0.25), residues: 407 sheet: -0.16 (0.40), residues: 149 loop : 0.86 (0.31), residues: 438 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 0.011 0.001 PHE B 347 TYR 0.013 0.001 TYR B 616 ARG 0.003 0.000 ARG A 275 *********************** 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: 6 poor density : 67 time to evaluate : 1.588 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: 0.9348 (m) cc_final: 0.9010 (t) REVERT: A 102 MET cc_start: 0.9050 (mmp) cc_final: 0.8647 (mmp) REVERT: B 743 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7252 (m-80) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.4140 time to fit residues: 40.8971 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 : 1.494 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.079067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059374 restraints weight = 67381.576| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.64 r_work: 0.2937 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3622 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= 0.154 Angle : 0.488 5.879 11191 Z= 0.251 Chirality : 0.042 0.140 1183 Planarity : 0.004 0.043 1462 Dihedral : 4.297 16.231 1112 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.49 % Allowed : 7.67 % Favored : 91.84 % 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: 1.93 (0.27), residues: 994 helix: 2.23 (0.25), residues: 407 sheet: -0.15 (0.40), residues: 150 loop : 1.08 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.004 0.001 HIS B 233 PHE 0.010 0.001 PHE B 347 TYR 0.011 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 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 1.345 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: 0.9323 (m) cc_final: 0.8998 (t) REVERT: B 56 MET cc_start: 0.8826 (mmm) cc_final: 0.8425 (mmm) REVERT: B 87 ASP cc_start: 0.8830 (t70) cc_final: 0.8550 (t70) REVERT: B 743 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7260 (m-80) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.3976 time to fit residues: 40.0808 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 : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 721 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 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.077828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058153 restraints weight = 67577.284| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.56 r_work: 0.2910 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3817 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= 0.287 Angle : 0.513 5.339 11191 Z= 0.269 Chirality : 0.042 0.138 1183 Planarity : 0.004 0.041 1462 Dihedral : 4.302 17.572 1112 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.49 % Allowed : 8.04 % Favored : 91.47 % 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: 1.81 (0.27), residues: 994 helix: 2.24 (0.25), residues: 407 sheet: -0.28 (0.40), residues: 148 loop : 0.92 (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 250 PHE 0.014 0.001 PHE A 37 TYR 0.010 0.001 TYR A 31 ARG 0.005 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 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.282 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: 0.9364 (m) cc_final: 0.9036 (t) REVERT: A 102 MET cc_start: 0.9030 (mmp) cc_final: 0.8811 (mmp) REVERT: B 56 MET cc_start: 0.8843 (mmm) cc_final: 0.8498 (mmm) REVERT: B 87 ASP cc_start: 0.8890 (t70) cc_final: 0.8584 (t70) REVERT: B 743 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: B 791 GLU cc_start: 0.9300 (tt0) cc_final: 0.9065 (pm20) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.3727 time to fit residues: 36.0140 Evaluate side-chains 66 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.077387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057941 restraints weight = 67658.880| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.55 r_work: 0.2907 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8236 Z= 0.269 Angle : 0.506 5.385 11191 Z= 0.265 Chirality : 0.042 0.138 1183 Planarity : 0.004 0.043 1462 Dihedral : 4.259 17.097 1112 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.73 % Allowed : 8.04 % Favored : 91.23 % 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: 1.80 (0.27), residues: 994 helix: 2.27 (0.25), residues: 407 sheet: -0.36 (0.39), residues: 148 loop : 0.90 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.004 0.001 HIS B 250 PHE 0.012 0.001 PHE B 347 TYR 0.011 0.001 TYR A 31 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 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.751 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: 0.9366 (m) cc_final: 0.9046 (t) REVERT: A 102 MET cc_start: 0.9117 (mmp) cc_final: 0.8839 (mmp) REVERT: B 680 MET cc_start: 0.8826 (mtp) cc_final: 0.8499 (mtp) REVERT: B 743 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7223 (m-80) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.4148 time to fit residues: 37.8985 Evaluate side-chains 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.077698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058054 restraints weight = 68302.350| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.62 r_work: 0.2909 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3997 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= 0.225 Angle : 0.497 5.538 11191 Z= 0.256 Chirality : 0.041 0.134 1183 Planarity : 0.004 0.042 1462 Dihedral : 4.174 17.775 1112 Min Nonbonded Distance : 2.145 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: 1.92 (0.27), residues: 994 helix: 2.42 (0.25), residues: 407 sheet: -0.39 (0.39), residues: 148 loop : 0.95 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.003 0.001 HIS A 351 PHE 0.012 0.001 PHE A 37 TYR 0.010 0.001 TYR B 616 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 : 1.328 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: 0.9345 (m) cc_final: 0.9006 (t) REVERT: A 102 MET cc_start: 0.9111 (mmp) cc_final: 0.8823 (mmp) REVERT: B 743 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: B 791 GLU cc_start: 0.9305 (tt0) cc_final: 0.9092 (pm20) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.3945 time to fit residues: 38.2467 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 : 1.288 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.078120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058636 restraints weight = 67230.572| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.56 r_work: 0.2924 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 8236 Z= 0.186 Angle : 0.478 5.711 11191 Z= 0.245 Chirality : 0.041 0.138 1183 Planarity : 0.004 0.043 1462 Dihedral : 4.055 18.256 1112 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.49 % Allowed : 8.28 % Favored : 91.23 % 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: 2.14 (0.28), residues: 994 helix: 2.60 (0.26), residues: 407 sheet: -0.27 (0.40), residues: 149 loop : 1.06 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 309 HIS 0.003 0.001 HIS A 38 PHE 0.013 0.001 PHE A 37 TYR 0.010 0.001 TYR B 616 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 70 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.309 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: 0.9312 (m) cc_final: 0.8989 (t) REVERT: A 102 MET cc_start: 0.9119 (mmp) cc_final: 0.8821 (mmp) REVERT: B 743 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 791 GLU cc_start: 0.9287 (tt0) cc_final: 0.9066 (pm20) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.3693 time to fit residues: 37.8678 Evaluate side-chains 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.078736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059358 restraints weight = 67120.058| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.59 r_work: 0.2941 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8236 Z= 0.131 Angle : 0.468 5.538 11191 Z= 0.236 Chirality : 0.041 0.141 1183 Planarity : 0.004 0.042 1462 Dihedral : 3.963 17.622 1112 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.24 % Allowed : 9.01 % 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: 2.28 (0.27), residues: 994 helix: 2.73 (0.26), residues: 405 sheet: -0.15 (0.40), residues: 149 loop : 1.13 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.003 0.001 HIS A 38 PHE 0.013 0.001 PHE A 37 TYR 0.012 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: 6910.16 seconds wall clock time: 125 minutes 49.65 seconds (7549.65 seconds total)