Starting phenix.real_space_refine on Thu Sep 18 15:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.map" model { file = "/net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fms_50566/09_2025/9fms_50566.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.015 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 37 5.16 5 C 5755 2.51 5 N 1519 2.21 5 O 1651 1.98 5 H 8842 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17805 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 11501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 11501 Classifications: {'peptide': 712} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 51, 'TRANS': 660} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 6121 Classifications: {'peptide': 377} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 365} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3.35, per 1000 atoms: 0.19 Number of scatterers: 17805 At special positions: 0 Unit cell: (80.1422, 88.9383, 139.76, 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 37 16.00 Mg 1 11.99 O 1651 8.00 N 1519 7.00 C 5755 6.00 H 8842 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 541.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 48.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 35 through 39 removed outlier: 4.459A pdb=" N TYR B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 106 through 135 removed outlier: 4.714A pdb=" N GLN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.978A pdb=" N ALA B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.957A pdb=" N GLU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 343 through 359 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 373 through 407 removed outlier: 3.526A pdb=" N ARG B 387 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 597 removed outlier: 3.798A pdb=" N PHE B 596 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 614 removed outlier: 3.887A pdb=" N ARG B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 645 removed outlier: 3.572A pdb=" N ASP B 626 " --> pdb=" O GLN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 681 through 688 Processing helix chain 'B' and resid 691 through 698 removed outlier: 4.775A pdb=" N HIS B 696 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.934A pdb=" N ARG B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 742 through 752 removed outlier: 3.589A pdb=" N ALA B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 757 Processing helix chain 'B' and resid 758 through 763 Processing helix chain 'B' and resid 780 through 789 Processing helix chain 'B' and resid 838 through 842 removed outlier: 4.383A pdb=" N THR B 841 " --> pdb=" O LEU B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 882 Processing helix chain 'B' and resid 894 through 899 Processing helix chain 'B' and resid 900 through 902 No H-bonds generated for 'chain 'B' and resid 900 through 902' Processing helix chain 'B' and resid 920 through 931 removed outlier: 3.797A pdb=" N PHE B 925 " --> pdb=" O TYR B 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 79 through 92 removed outlier: 4.077A pdb=" N HIS A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.602A pdb=" N ASN A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.689A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.632A pdb=" N HIS A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.700A pdb=" N VAL A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.681A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 377 through 386 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.515A pdb=" N HIS B 227 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 251 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 229 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU B 253 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N CYS B 228 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B 49 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR B 230 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR B 51 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU B 47 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 96 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN B 49 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 98 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR B 51 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA B 100 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP B 53 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 367 through 368 Processing sheet with id=AA3, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.854A pdb=" N THR D 11 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN A 20 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU D 13 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LYS A 22 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN A 20 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY A 210 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 206 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 26 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 204 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 101 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLY A 219 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR A 103 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU A 221 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 104 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU A 139 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.854A pdb=" N THR D 11 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN A 20 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU D 13 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LYS A 22 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.847A pdb=" N ASN A 44 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS A 224 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 239 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE A 277 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A 241 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY A 279 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A 243 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N LYS A 281 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 289 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.930A pdb=" N LYS A 67 " --> pdb=" O HIS A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 379 hydrogen bonds defined for protein. 1029 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: 3.93 Time building geometry restraints manager: 2.05 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: 8826 1.13 - 1.30: 1589 1.30 - 1.47: 3512 1.47 - 1.65: 4042 1.65 - 1.82: 58 Bond restraints: 18027 Sorted by residual: bond pdb=" CD2 HIS B 383 " pdb=" HD2 HIS B 383 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE ARG B 783 " pdb=" HE ARG B 783 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N CYS B 646 " pdb=" H CYS B 646 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N PHE A 226 " pdb=" H PHE A 226 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS B 282 " pdb=" H LYS B 282 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 18022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 27784 2.65 - 5.30: 3756 5.30 - 7.95: 995 7.95 - 10.60: 33 10.60 - 13.25: 17 Bond angle restraints: 32585 Sorted by residual: angle pdb=" N ASP B 197 " pdb=" CA ASP B 197 " pdb=" CB ASP B 197 " ideal model delta sigma weight residual 110.29 101.42 8.87 1.36e+00 5.41e-01 4.25e+01 angle pdb=" C GLY A 133 " pdb=" N GLN A 134 " pdb=" CA GLN A 134 " ideal model delta sigma weight residual 121.62 132.94 -11.32 1.83e+00 2.99e-01 3.83e+01 angle pdb=" CA PHE A 348 " pdb=" CB PHE A 348 " pdb=" CG PHE A 348 " ideal model delta sigma weight residual 113.80 119.31 -5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" OE1 GLN B 913 " pdb=" CD GLN B 913 " pdb=" NE2 GLN B 913 " ideal model delta sigma weight residual 122.60 117.38 5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" OE1 GLN B 215 " pdb=" CD GLN B 215 " pdb=" NE2 GLN B 215 " ideal model delta sigma weight residual 122.60 117.51 5.09 1.00e+00 1.00e+00 2.59e+01 ... (remaining 32580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 7725 17.54 - 35.07: 478 35.07 - 52.61: 155 52.61 - 70.15: 132 70.15 - 87.69: 14 Dihedral angle restraints: 8504 sinusoidal: 4603 harmonic: 3901 Sorted by residual: dihedral pdb=" CA PRO B 43 " pdb=" C PRO B 43 " pdb=" N ASN B 44 " pdb=" CA ASN B 44 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N HIS A 284 " pdb=" CA HIS A 284 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA CYS A 244 " pdb=" C CYS A 244 " pdb=" N THR A 245 " pdb=" CA THR A 245 " ideal model delta harmonic sigma weight residual 180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 8501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 800 0.081 - 0.163: 411 0.163 - 0.244: 95 0.244 - 0.325: 19 0.325 - 0.406: 5 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA LYS B 845 " pdb=" N LYS B 845 " pdb=" C LYS B 845 " pdb=" CB LYS B 845 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA TRP A 326 " pdb=" N TRP A 326 " pdb=" C TRP A 326 " pdb=" CB TRP A 326 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA HIS B 244 " pdb=" N HIS B 244 " pdb=" C HIS B 244 " pdb=" CB HIS B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1327 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 803 " 0.158 2.00e-02 2.50e+03 1.53e-01 3.53e+02 pdb=" CD GLN B 803 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN B 803 " -0.100 2.00e-02 2.50e+03 pdb=" NE2 GLN B 803 " -0.148 2.00e-02 2.50e+03 pdb="HE21 GLN B 803 " -0.121 2.00e-02 2.50e+03 pdb="HE22 GLN B 803 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 651 " 0.210 2.00e-02 2.50e+03 8.15e-02 2.66e+02 pdb=" CG TRP B 651 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP B 651 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 651 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP B 651 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP B 651 " -0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP B 651 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 651 " 0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 651 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 651 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP B 651 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP B 651 " -0.095 2.00e-02 2.50e+03 pdb=" HE3 TRP B 651 " -0.111 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 651 " 0.066 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 651 " -0.023 2.00e-02 2.50e+03 pdb=" HH2 TRP B 651 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 230 " -0.203 2.00e-02 2.50e+03 8.31e-02 2.07e+02 pdb=" CG TYR B 230 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR B 230 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR B 230 " 0.100 2.00e-02 2.50e+03 pdb=" CE1 TYR B 230 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR B 230 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 230 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR B 230 " -0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR B 230 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR B 230 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR B 230 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR B 230 " -0.088 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 978 2.18 - 2.78: 30796 2.78 - 3.39: 49153 3.39 - 3.99: 64558 3.99 - 4.60: 94937 Nonbonded interactions: 240422 Sorted by model distance: nonbonded pdb=" HH TYR B 657 " pdb=" OD2 ASP B 724 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR B 221 " pdb=" OE1 GLU B 245 " model vdw 1.589 2.450 nonbonded pdb=" HG SER B 5 " pdb=" OE1 GLU B 345 " model vdw 1.601 2.450 nonbonded pdb=" OE2 GLU B 203 " pdb=" HH TYR B 641 " model vdw 1.613 2.450 nonbonded pdb=" OE2 GLU A 23 " pdb=" HG SER A 205 " model vdw 1.621 2.450 ... (remaining 240417 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.220 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 0.091 9185 Z= 0.741 Angle : 1.829 11.319 12432 Z= 1.236 Chirality : 0.098 0.406 1330 Planarity : 0.016 0.165 1613 Dihedral : 14.004 87.685 3442 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.20 % Allowed : 4.38 % Favored : 95.42 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.23), residues: 1084 helix: -1.52 (0.21), residues: 421 sheet: 0.65 (0.45), residues: 114 loop : -0.50 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 175 TYR 0.181 0.022 TYR B 230 PHE 0.101 0.014 PHE B 7 TRP 0.139 0.026 TRP B 651 HIS 0.011 0.003 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.01214 ( 9185) covalent geometry : angle 1.82939 (12432) hydrogen bonds : bond 0.19764 ( 379) hydrogen bonds : angle 7.42599 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.522 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: B 54 MET cc_start: 0.8753 (tpp) cc_final: 0.8522 (mmm) REVERT: B 361 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8480 (mtpt) REVERT: B 678 THR cc_start: 0.9101 (m) cc_final: 0.8829 (p) REVERT: A 37 ILE cc_start: 0.9192 (pt) cc_final: 0.8969 (mm) REVERT: A 213 ASN cc_start: 0.8059 (p0) cc_final: 0.6890 (p0) REVERT: A 283 ASP cc_start: 0.8090 (m-30) cc_final: 0.7581 (m-30) REVERT: A 346 LEU cc_start: 0.7464 (mt) cc_final: 0.6848 (mt) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 1.3808 time to fit residues: 271.7458 Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 122 ASN A 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078365 restraints weight = 47386.064| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.35 r_work: 0.2963 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9185 Z= 0.170 Angle : 0.723 8.094 12432 Z= 0.394 Chirality : 0.044 0.166 1330 Planarity : 0.006 0.072 1613 Dihedral : 6.829 61.397 1201 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.63 % Allowed : 10.79 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.24), residues: 1084 helix: 0.05 (0.24), residues: 428 sheet: 0.45 (0.43), residues: 127 loop : -0.35 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 318 TYR 0.022 0.002 TYR B 230 PHE 0.032 0.002 PHE A 348 TRP 0.017 0.002 TRP B 732 HIS 0.006 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9185) covalent geometry : angle 0.72305 (12432) hydrogen bonds : bond 0.05916 ( 379) hydrogen bonds : angle 5.50257 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.537 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: B 42 ASN cc_start: 0.6231 (t0) cc_final: 0.5929 (t0) REVERT: B 361 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8336 (mtpt) REVERT: B 869 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8673 (mm-30) REVERT: A 100 ASP cc_start: 0.8370 (m-30) cc_final: 0.7823 (m-30) REVERT: A 221 GLU cc_start: 0.8321 (tt0) cc_final: 0.7898 (mt-10) REVERT: A 259 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7257 (mmt180) REVERT: A 282 ASP cc_start: 0.7820 (t0) cc_final: 0.7578 (t0) REVERT: A 283 ASP cc_start: 0.8222 (m-30) cc_final: 0.7178 (m-30) REVERT: A 359 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6523 (mt-10) outliers start: 16 outliers final: 4 residues processed: 115 average time/residue: 1.0720 time to fit residues: 132.7405 Evaluate side-chains 97 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079361 restraints weight = 47641.891| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.34 r_work: 0.2976 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9185 Z= 0.150 Angle : 0.617 7.031 12432 Z= 0.328 Chirality : 0.042 0.168 1330 Planarity : 0.005 0.056 1613 Dihedral : 6.066 54.767 1201 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.73 % Allowed : 11.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1084 helix: 0.76 (0.25), residues: 424 sheet: 0.14 (0.42), residues: 127 loop : -0.22 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 342 TYR 0.017 0.001 TYR B 230 PHE 0.043 0.001 PHE A 344 TRP 0.017 0.002 TRP B 732 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9185) covalent geometry : angle 0.61660 (12432) hydrogen bonds : bond 0.04669 ( 379) hydrogen bonds : angle 5.03509 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.456 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: B 75 GLU cc_start: 0.8099 (tt0) cc_final: 0.7704 (tm-30) REVERT: B 361 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8362 (mtpt) REVERT: B 601 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 869 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8661 (tp30) REVERT: A 100 ASP cc_start: 0.8390 (m-30) cc_final: 0.7838 (m-30) REVERT: A 131 PHE cc_start: 0.7580 (p90) cc_final: 0.7092 (p90) REVERT: A 221 GLU cc_start: 0.8253 (tt0) cc_final: 0.7938 (mt-10) REVERT: A 259 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7264 (mmt180) REVERT: A 283 ASP cc_start: 0.8174 (m-30) cc_final: 0.7587 (m-30) REVERT: A 354 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8187 (mtm-85) REVERT: A 359 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7064 (mt-10) outliers start: 17 outliers final: 2 residues processed: 109 average time/residue: 1.0431 time to fit residues: 122.7141 Evaluate side-chains 96 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 101 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080492 restraints weight = 47295.611| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.30 r_work: 0.2995 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9185 Z= 0.112 Angle : 0.557 7.057 12432 Z= 0.294 Chirality : 0.040 0.170 1330 Planarity : 0.005 0.050 1613 Dihedral : 5.577 50.859 1201 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.22 % Allowed : 12.42 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1084 helix: 1.23 (0.25), residues: 424 sheet: 0.06 (0.42), residues: 127 loop : -0.13 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 342 TYR 0.013 0.001 TYR B 230 PHE 0.027 0.001 PHE A 344 TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9185) covalent geometry : angle 0.55706 (12432) hydrogen bonds : bond 0.04056 ( 379) hydrogen bonds : angle 4.78743 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 MET cc_start: 0.8464 (mmp) cc_final: 0.8084 (mmt) REVERT: B 361 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8383 (mtpt) REVERT: A 100 ASP cc_start: 0.8379 (m-30) cc_final: 0.7801 (m-30) REVERT: A 221 GLU cc_start: 0.8191 (tt0) cc_final: 0.7940 (mt-10) REVERT: A 259 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7256 (mmt180) REVERT: A 283 ASP cc_start: 0.7627 (m-30) cc_final: 0.7368 (m-30) REVERT: A 297 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 354 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8167 (mtm-85) REVERT: A 359 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7215 (mt-10) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.9995 time to fit residues: 107.2660 Evaluate side-chains 92 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078796 restraints weight = 47385.264| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.28 r_work: 0.2960 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9185 Z= 0.159 Angle : 0.572 7.372 12432 Z= 0.300 Chirality : 0.041 0.171 1330 Planarity : 0.005 0.048 1613 Dihedral : 5.424 50.310 1201 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.63 % Allowed : 12.73 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1084 helix: 1.40 (0.26), residues: 424 sheet: -0.07 (0.42), residues: 129 loop : -0.10 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 342 TYR 0.018 0.001 TYR B 38 PHE 0.024 0.001 PHE A 344 TRP 0.013 0.001 TRP B 732 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9185) covalent geometry : angle 0.57158 (12432) hydrogen bonds : bond 0.04114 ( 379) hydrogen bonds : angle 4.71535 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.513 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: B 361 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8399 (mtpt) REVERT: A 100 ASP cc_start: 0.8340 (m-30) cc_final: 0.7750 (m-30) REVERT: A 187 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7799 (pp20) REVERT: A 221 GLU cc_start: 0.8242 (tt0) cc_final: 0.7978 (mt-10) REVERT: A 259 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7317 (mmt180) REVERT: A 323 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 340 GLN cc_start: 0.8542 (tt0) cc_final: 0.8324 (tt0) REVERT: A 354 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7912 (mtm-85) REVERT: A 359 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7187 (mt-10) outliers start: 16 outliers final: 5 residues processed: 99 average time/residue: 0.9629 time to fit residues: 103.6396 Evaluate side-chains 94 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN B 614 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078242 restraints weight = 47161.470| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.28 r_work: 0.2956 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9185 Z= 0.160 Angle : 0.566 7.803 12432 Z= 0.294 Chirality : 0.041 0.161 1330 Planarity : 0.005 0.045 1613 Dihedral : 5.281 45.143 1201 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.93 % Allowed : 13.34 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1084 helix: 1.51 (0.26), residues: 424 sheet: -0.16 (0.42), residues: 129 loop : -0.15 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 342 TYR 0.012 0.001 TYR A 285 PHE 0.025 0.001 PHE A 344 TRP 0.016 0.001 TRP B 732 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9185) covalent geometry : angle 0.56594 (12432) hydrogen bonds : bond 0.04031 ( 379) hydrogen bonds : angle 4.63285 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8361 (mtpt) REVERT: A 100 ASP cc_start: 0.8360 (m-30) cc_final: 0.7762 (m-30) REVERT: A 131 PHE cc_start: 0.7423 (p90) cc_final: 0.7219 (p90) REVERT: A 221 GLU cc_start: 0.8250 (tt0) cc_final: 0.7985 (mt-10) REVERT: A 259 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7301 (mmt180) REVERT: A 308 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 323 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 354 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7883 (mtm-85) REVERT: A 359 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7346 (mt-10) outliers start: 19 outliers final: 8 residues processed: 98 average time/residue: 1.0128 time to fit residues: 107.8236 Evaluate side-chains 95 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077979 restraints weight = 47776.322| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.29 r_work: 0.2951 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9185 Z= 0.158 Angle : 0.574 7.757 12432 Z= 0.298 Chirality : 0.041 0.161 1330 Planarity : 0.005 0.050 1613 Dihedral : 5.164 43.457 1201 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.32 % Allowed : 13.95 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1084 helix: 1.55 (0.26), residues: 424 sheet: -0.17 (0.43), residues: 129 loop : -0.17 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 342 TYR 0.012 0.001 TYR A 285 PHE 0.020 0.001 PHE A 344 TRP 0.009 0.001 TRP B 291 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9185) covalent geometry : angle 0.57444 (12432) hydrogen bonds : bond 0.03959 ( 379) hydrogen bonds : angle 4.60138 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.346 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: B 361 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8389 (mtpt) REVERT: A 202 GLU cc_start: 0.7807 (mp0) cc_final: 0.7240 (mm-30) REVERT: A 259 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7296 (mmt180) REVERT: A 308 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 323 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 340 GLN cc_start: 0.8674 (tt0) cc_final: 0.8433 (tm-30) REVERT: A 359 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7226 (mt-10) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.9990 time to fit residues: 101.3998 Evaluate side-chains 95 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077587 restraints weight = 47489.196| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.28 r_work: 0.2944 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9185 Z= 0.157 Angle : 0.563 7.954 12432 Z= 0.293 Chirality : 0.041 0.157 1330 Planarity : 0.005 0.055 1613 Dihedral : 5.079 41.266 1201 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.32 % Allowed : 14.15 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1084 helix: 1.58 (0.26), residues: 425 sheet: -0.22 (0.43), residues: 129 loop : -0.20 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 342 TYR 0.015 0.001 TYR B 882 PHE 0.023 0.001 PHE A 348 TRP 0.009 0.001 TRP B 291 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9185) covalent geometry : angle 0.56338 (12432) hydrogen bonds : bond 0.03899 ( 379) hydrogen bonds : angle 4.57523 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8437 (mtpt) REVERT: B 594 ASP cc_start: 0.8846 (t70) cc_final: 0.8427 (OUTLIER) REVERT: A 202 GLU cc_start: 0.7808 (mp0) cc_final: 0.7190 (mp0) REVERT: A 259 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7300 (mmt180) REVERT: A 308 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 323 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 359 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7274 (mt-10) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 1.0182 time to fit residues: 108.1790 Evaluate side-chains 94 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.102019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077351 restraints weight = 47700.763| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.25 r_work: 0.2939 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9185 Z= 0.174 Angle : 0.583 8.513 12432 Z= 0.306 Chirality : 0.041 0.161 1330 Planarity : 0.005 0.070 1613 Dihedral : 5.093 40.944 1201 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.32 % Allowed : 14.66 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1084 helix: 1.55 (0.26), residues: 425 sheet: -0.24 (0.43), residues: 129 loop : -0.18 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 342 TYR 0.013 0.001 TYR A 285 PHE 0.022 0.001 PHE A 344 TRP 0.009 0.001 TRP B 291 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9185) covalent geometry : angle 0.58320 (12432) hydrogen bonds : bond 0.03975 ( 379) hydrogen bonds : angle 4.57973 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.516 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: B 361 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8396 (mtpt) REVERT: B 594 ASP cc_start: 0.8860 (t70) cc_final: 0.8436 (OUTLIER) REVERT: A 131 PHE cc_start: 0.7294 (p90) cc_final: 0.7022 (p90) REVERT: A 202 GLU cc_start: 0.7767 (mp0) cc_final: 0.7226 (mm-30) REVERT: A 259 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7316 (mmt180) REVERT: A 308 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 323 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 359 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7320 (mt-10) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 1.0476 time to fit residues: 105.6090 Evaluate side-chains 92 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.102705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078111 restraints weight = 47398.573| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.25 r_work: 0.2955 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9185 Z= 0.136 Angle : 0.565 9.255 12432 Z= 0.293 Chirality : 0.041 0.159 1330 Planarity : 0.005 0.067 1613 Dihedral : 4.974 38.559 1201 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.81 % Allowed : 15.07 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.26), residues: 1084 helix: 1.68 (0.26), residues: 424 sheet: -0.33 (0.44), residues: 124 loop : -0.09 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 342 TYR 0.013 0.001 TYR B 176 PHE 0.020 0.001 PHE A 344 TRP 0.019 0.001 TRP B 732 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9185) covalent geometry : angle 0.56456 (12432) hydrogen bonds : bond 0.03751 ( 379) hydrogen bonds : angle 4.50866 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.384 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: B 361 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8442 (mtpt) REVERT: B 594 ASP cc_start: 0.8834 (t70) cc_final: 0.8495 (t0) REVERT: B 835 LEU cc_start: 0.7258 (mp) cc_final: 0.6622 (pt) REVERT: A 100 ASP cc_start: 0.8547 (m-30) cc_final: 0.8200 (m-30) REVERT: A 131 PHE cc_start: 0.7211 (p90) cc_final: 0.6977 (p90) REVERT: A 202 GLU cc_start: 0.7754 (mp0) cc_final: 0.7379 (mm-30) REVERT: A 259 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7294 (mmt180) REVERT: A 308 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 323 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7854 (tp) REVERT: A 359 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7367 (mt-10) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 1.0395 time to fit residues: 101.5024 Evaluate side-chains 91 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 62 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 605 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079690 restraints weight = 47240.345| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.28 r_work: 0.2978 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9185 Z= 0.107 Angle : 0.547 9.265 12432 Z= 0.282 Chirality : 0.040 0.161 1330 Planarity : 0.005 0.063 1613 Dihedral : 4.772 34.535 1201 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.92 % Allowed : 15.07 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1084 helix: 1.83 (0.26), residues: 424 sheet: -0.38 (0.43), residues: 124 loop : 0.05 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 342 TYR 0.021 0.001 TYR B 176 PHE 0.020 0.001 PHE A 344 TRP 0.015 0.001 TRP A 326 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9185) covalent geometry : angle 0.54718 (12432) hydrogen bonds : bond 0.03432 ( 379) hydrogen bonds : angle 4.42815 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5022.52 seconds wall clock time: 85 minutes 38.74 seconds (5138.74 seconds total)