Starting phenix.real_space_refine on Wed Jan 22 04:35:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fms_50566/01_2025/9fms_50566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fms_50566/01_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_50566/01_2025/9fms_50566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fms_50566/01_2025/9fms_50566.map" model { file = "/net/cci-nas-00/data/ceres_data/9fms_50566/01_2025/9fms_50566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fms_50566/01_2025/9fms_50566.cif" } resolution = 2.65 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.54, per 1000 atoms: 0.48 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: 4.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.53 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: 6.95 Time building geometry restraints manager: 5.36 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: 3.700 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: 0.270 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.140 ------------------------------------------------------------------------------- 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= 0.788 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), 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 TRP 0.139 0.026 TRP B 651 HIS 0.011 0.003 HIS A 338 PHE 0.101 0.014 PHE B 7 TYR 0.181 0.022 TYR B 230 ARG 0.011 0.001 ARG B 175 *********************** 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 : 1.422 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: B 54 MET cc_start: 0.8753 (tpp) cc_final: 0.8521 (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: 2.9174 time to fit residues: 577.3110 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 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 = 0.3543 r_free = 0.3543 target = 0.104701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.079511 restraints weight = 47357.454| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.31 r_work: 0.2979 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9185 Z= 0.248 Angle : 0.697 7.664 12432 Z= 0.377 Chirality : 0.044 0.164 1330 Planarity : 0.006 0.069 1613 Dihedral : 6.720 57.770 1201 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.63 % Allowed : 10.90 % Favored : 87.47 % 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: -0.17 (0.24), residues: 1084 helix: 0.13 (0.24), residues: 428 sheet: 0.39 (0.42), residues: 127 loop : -0.33 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 732 HIS 0.006 0.001 HIS B 206 PHE 0.030 0.002 PHE A 348 TYR 0.022 0.002 TYR B 176 ARG 0.006 0.001 ARG B 318 *********************** 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 125 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 MET cc_start: 0.8864 (tpp) cc_final: 0.8531 (mmm) REVERT: B 317 GLU cc_start: 0.8026 (mp0) cc_final: 0.7749 (mm-30) REVERT: B 361 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8346 (mtpt) REVERT: B 869 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8680 (mm-30) REVERT: A 100 ASP cc_start: 0.8364 (m-30) cc_final: 0.7843 (m-30) REVERT: A 221 GLU cc_start: 0.8275 (tt0) cc_final: 0.7877 (mt-10) REVERT: A 233 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7930 (mmm-85) REVERT: A 259 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7165 (mmt180) REVERT: A 282 ASP cc_start: 0.7828 (t0) cc_final: 0.7605 (t0) REVERT: A 283 ASP cc_start: 0.8253 (m-30) cc_final: 0.7220 (m-30) REVERT: A 359 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6424 (mt-10) outliers start: 16 outliers final: 3 residues processed: 117 average time/residue: 2.3755 time to fit residues: 300.4778 Evaluate side-chains 97 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain A residue 354 ARG 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 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 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 = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078988 restraints weight = 47226.973| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.31 r_work: 0.2968 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9185 Z= 0.235 Angle : 0.615 7.218 12432 Z= 0.328 Chirality : 0.042 0.166 1330 Planarity : 0.005 0.056 1613 Dihedral : 6.044 55.006 1201 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.53 % Allowed : 11.61 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.25), residues: 1084 helix: 0.78 (0.25), residues: 424 sheet: 0.17 (0.42), residues: 127 loop : -0.25 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 732 HIS 0.004 0.001 HIS B 337 PHE 0.038 0.002 PHE A 344 TYR 0.018 0.001 TYR B 230 ARG 0.010 0.001 ARG A 342 *********************** 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 114 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.137 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 54 MET cc_start: 0.8803 (tpp) cc_final: 0.8593 (mmm) REVERT: B 75 GLU cc_start: 0.8096 (tt0) cc_final: 0.7699 (tm-30) REVERT: B 205 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 361 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8361 (mtpt) REVERT: B 601 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: B 869 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8659 (tp30) REVERT: A 100 ASP cc_start: 0.8385 (m-30) cc_final: 0.7851 (m-30) REVERT: A 131 PHE cc_start: 0.7511 (p90) cc_final: 0.7263 (p90) REVERT: A 221 GLU cc_start: 0.8260 (tt0) cc_final: 0.7944 (mt-10) REVERT: A 233 ARG cc_start: 0.8376 (mtp85) cc_final: 0.8096 (mmm-85) REVERT: A 259 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7294 (mmt180) REVERT: A 283 ASP cc_start: 0.8149 (m-30) cc_final: 0.7549 (m-30) REVERT: A 359 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7002 (mt-10) outliers start: 15 outliers final: 2 residues processed: 109 average time/residue: 2.4813 time to fit residues: 291.2269 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 : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU 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 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 105 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 902 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078376 restraints weight = 47247.514| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.29 r_work: 0.2954 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9185 Z= 0.244 Angle : 0.578 6.357 12432 Z= 0.307 Chirality : 0.041 0.167 1330 Planarity : 0.005 0.051 1613 Dihedral : 5.649 52.502 1201 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.12 % Allowed : 12.53 % 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 (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: 0.49 (0.25), residues: 1084 helix: 1.17 (0.25), residues: 424 sheet: 0.00 (0.42), residues: 129 loop : -0.21 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 732 HIS 0.004 0.001 HIS A 284 PHE 0.025 0.001 PHE A 344 TYR 0.013 0.001 TYR A 285 ARG 0.008 0.000 ARG A 342 *********************** 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 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.572 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 54 MET cc_start: 0.8734 (tpp) cc_final: 0.8514 (mmm) REVERT: B 205 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 295 ASN cc_start: 0.8356 (t0) cc_final: 0.8070 (t0) REVERT: B 361 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8384 (mtpt) REVERT: A 100 ASP cc_start: 0.8360 (m-30) cc_final: 0.7785 (m-30) REVERT: A 221 GLU cc_start: 0.8278 (tt0) cc_final: 0.7981 (mt-10) REVERT: A 233 ARG cc_start: 0.8350 (mtp85) cc_final: 0.8066 (mmm-85) REVERT: A 259 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7273 (mmt180) REVERT: A 283 ASP cc_start: 0.7695 (m-30) cc_final: 0.7402 (m-30) REVERT: A 323 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7808 (tp) REVERT: A 330 MET cc_start: 0.5035 (mtt) cc_final: 0.4769 (mpp) REVERT: A 359 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7170 (mt-10) outliers start: 11 outliers final: 3 residues processed: 104 average time/residue: 2.2712 time to fit residues: 256.2220 Evaluate side-chains 95 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU 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 359 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 104 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 61 optimal weight: 0.0020 overall best weight: 0.1966 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.105701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080950 restraints weight = 47567.364| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.30 r_work: 0.3008 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9185 Z= 0.153 Angle : 0.544 7.361 12432 Z= 0.282 Chirality : 0.040 0.172 1330 Planarity : 0.004 0.046 1613 Dihedral : 5.223 43.818 1201 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.02 % Allowed : 14.15 % Favored : 84.83 % 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: 0.79 (0.25), residues: 1084 helix: 1.51 (0.26), residues: 424 sheet: -0.07 (0.41), residues: 129 loop : -0.04 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 732 HIS 0.002 0.001 HIS A 92 PHE 0.026 0.001 PHE A 344 TYR 0.017 0.001 TYR B 38 ARG 0.011 0.000 ARG A 342 *********************** 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 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.448 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: 0.8811 (mmtt) cc_final: 0.8398 (mtpt) REVERT: A 100 ASP cc_start: 0.8323 (m-30) cc_final: 0.7775 (m-30) REVERT: A 131 PHE cc_start: 0.7301 (p90) cc_final: 0.6923 (p90) REVERT: A 221 GLU cc_start: 0.8146 (tt0) cc_final: 0.7926 (mt-10) REVERT: A 233 ARG cc_start: 0.8315 (mtp85) cc_final: 0.8035 (mmm-85) REVERT: A 259 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7305 (mmt180) REVERT: A 330 MET cc_start: 0.4719 (OUTLIER) cc_final: 0.4430 (mpp) REVERT: A 340 GLN cc_start: 0.8529 (tt0) cc_final: 0.8303 (tt0) REVERT: A 359 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7110 (mt-10) outliers start: 10 outliers final: 2 residues processed: 101 average time/residue: 2.2470 time to fit residues: 247.7686 Evaluate side-chains 91 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 CYS Chi-restraints excluded: chain B residue 398 GLN Chi-restraints excluded: chain A residue 330 MET 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 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.104265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079386 restraints weight = 47424.324| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.29 r_work: 0.2977 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9185 Z= 0.210 Angle : 0.549 7.248 12432 Z= 0.285 Chirality : 0.041 0.160 1330 Planarity : 0.004 0.059 1613 Dihedral : 5.096 41.653 1201 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.22 % Allowed : 13.85 % Favored : 84.93 % 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: 0.79 (0.26), residues: 1084 helix: 1.57 (0.26), residues: 425 sheet: -0.12 (0.42), residues: 129 loop : -0.10 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 732 HIS 0.009 0.001 HIS B 59 PHE 0.018 0.001 PHE A 344 TYR 0.011 0.001 TYR B 176 ARG 0.011 0.000 ARG A 342 *********************** 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 103 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 361 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8370 (mtpt) REVERT: A 100 ASP cc_start: 0.8320 (m-30) cc_final: 0.7728 (m-30) REVERT: A 131 PHE cc_start: 0.7272 (p90) cc_final: 0.7062 (p90) REVERT: A 221 GLU cc_start: 0.8224 (tt0) cc_final: 0.7989 (mt-10) REVERT: A 233 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8114 (mmm-85) REVERT: A 259 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7313 (mmt180) REVERT: A 308 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 323 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7843 (tp) REVERT: A 340 GLN cc_start: 0.8473 (tt0) cc_final: 0.8270 (tt0) REVERT: A 359 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7238 (mt-10) outliers start: 12 outliers final: 4 residues processed: 99 average time/residue: 2.2959 time to fit residues: 246.6892 Evaluate side-chains 94 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 205 GLU 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 359 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.103495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078596 restraints weight = 47422.606| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.28 r_work: 0.2962 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4616 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= 0.232 Angle : 0.559 7.570 12432 Z= 0.292 Chirality : 0.041 0.159 1330 Planarity : 0.005 0.054 1613 Dihedral : 5.040 41.383 1201 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.53 % Allowed : 13.65 % Favored : 84.83 % 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: 0.77 (0.26), residues: 1084 helix: 1.60 (0.26), residues: 425 sheet: -0.14 (0.42), residues: 129 loop : -0.15 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.003 0.001 HIS B 59 PHE 0.021 0.001 PHE A 344 TYR 0.012 0.001 TYR A 285 ARG 0.012 0.000 ARG A 342 *********************** 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 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.486 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: B 361 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8400 (mtpt) REVERT: B 594 ASP cc_start: 0.8858 (t70) cc_final: 0.8423 (OUTLIER) REVERT: A 100 ASP cc_start: 0.8338 (m-30) cc_final: 0.7734 (m-30) REVERT: A 202 GLU cc_start: 0.7828 (mp0) cc_final: 0.7262 (mm-30) REVERT: A 233 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8202 (mmm-85) REVERT: A 259 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7312 (mmt180) REVERT: A 308 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 323 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 359 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7218 (mt-10) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 2.3147 time to fit residues: 251.1270 Evaluate side-chains 96 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 11 GLN Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP 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 25 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.103224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078370 restraints weight = 47389.888| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.28 r_work: 0.2958 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4747 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= 0.212 Angle : 0.550 7.853 12432 Z= 0.286 Chirality : 0.040 0.158 1330 Planarity : 0.005 0.067 1613 Dihedral : 4.951 40.051 1201 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.12 % Allowed : 14.56 % Favored : 84.32 % 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: 0.78 (0.26), residues: 1084 helix: 1.64 (0.26), residues: 425 sheet: -0.21 (0.42), residues: 129 loop : -0.14 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 732 HIS 0.003 0.001 HIS B 59 PHE 0.021 0.001 PHE A 348 TYR 0.012 0.001 TYR A 285 ARG 0.012 0.000 ARG A 342 *********************** 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 99 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.396 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: 0.8829 (mmtt) cc_final: 0.8437 (mtpt) REVERT: B 594 ASP cc_start: 0.8854 (t70) cc_final: 0.8412 (OUTLIER) REVERT: B 835 LEU cc_start: 0.7238 (mp) cc_final: 0.6774 (pt) REVERT: A 202 GLU cc_start: 0.7822 (mp0) cc_final: 0.7281 (mm-30) REVERT: A 233 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8204 (mmm-85) REVERT: A 259 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7284 (mmt180) REVERT: A 308 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 323 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7851 (tp) REVERT: A 330 MET cc_start: 0.4185 (mtt) cc_final: 0.3906 (mpp) REVERT: A 359 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7270 (mt-10) outliers start: 11 outliers final: 6 residues processed: 96 average time/residue: 2.2047 time to fit residues: 230.0264 Evaluate side-chains 91 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 814 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.103371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078629 restraints weight = 47441.448| |-----------------------------------------------------------------------------| r_work (start): 0.3093 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: 0.7644 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9185 Z= 0.200 Angle : 0.552 8.339 12432 Z= 0.287 Chirality : 0.040 0.160 1330 Planarity : 0.005 0.072 1613 Dihedral : 4.879 38.328 1201 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 (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: 0.85 (0.26), residues: 1084 helix: 1.68 (0.26), residues: 426 sheet: -0.23 (0.42), residues: 129 loop : -0.08 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 291 HIS 0.003 0.001 HIS B 59 PHE 0.021 0.001 PHE A 344 TYR 0.014 0.001 TYR B 176 ARG 0.014 0.000 ARG A 342 *********************** 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 96 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.521 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: 0.8823 (mmtt) cc_final: 0.8435 (mtpt) REVERT: B 594 ASP cc_start: 0.8835 (t70) cc_final: 0.8418 (OUTLIER) REVERT: B 835 LEU cc_start: 0.7209 (mp) cc_final: 0.6803 (pt) REVERT: A 100 ASP cc_start: 0.8598 (m-30) cc_final: 0.8188 (m-30) REVERT: A 131 PHE cc_start: 0.7244 (p90) cc_final: 0.6805 (p90) REVERT: A 202 GLU cc_start: 0.7835 (mp0) cc_final: 0.7311 (mm-30) REVERT: A 233 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8217 (mmm-85) REVERT: A 259 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7292 (mmt180) REVERT: A 308 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 323 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 330 MET cc_start: 0.4117 (mtt) cc_final: 0.3860 (mpp) REVERT: A 359 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7326 (mt-10) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 2.3319 time to fit residues: 238.7920 Evaluate side-chains 92 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 814 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.103251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078557 restraints weight = 47398.658| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.28 r_work: 0.3031 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4896 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= 0.207 Angle : 0.551 9.385 12432 Z= 0.286 Chirality : 0.040 0.159 1330 Planarity : 0.004 0.063 1613 Dihedral : 4.823 37.216 1201 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.81 % Allowed : 15.27 % Favored : 83.91 % 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: 0.88 (0.26), residues: 1084 helix: 1.73 (0.26), residues: 425 sheet: -0.34 (0.43), residues: 124 loop : -0.05 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 732 HIS 0.002 0.001 HIS B 206 PHE 0.018 0.001 PHE A 348 TYR 0.022 0.001 TYR B 176 ARG 0.011 0.000 ARG A 342 ********************** 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 96 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.321 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: 0.8862 (mmtt) cc_final: 0.8479 (mtpt) REVERT: B 594 ASP cc_start: 0.8829 (t70) cc_final: 0.8484 (t0) REVERT: B 835 LEU cc_start: 0.7371 (mp) cc_final: 0.6740 (pt) REVERT: A 100 ASP cc_start: 0.8511 (m-30) cc_final: 0.8097 (m-30) REVERT: A 131 PHE cc_start: 0.7247 (p90) cc_final: 0.6910 (p90) REVERT: A 202 GLU cc_start: 0.7782 (mp0) cc_final: 0.7382 (mm-30) REVERT: A 233 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8273 (mmm-85) REVERT: A 259 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7286 (mmt180) REVERT: A 308 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8394 (tm-30) REVERT: A 323 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7866 (tp) REVERT: A 330 MET cc_start: 0.4049 (mtt) cc_final: 0.3793 (mpp) REVERT: A 359 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7551 (mt-10) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 2.2972 time to fit residues: 237.2077 Evaluate side-chains 94 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 814 SER Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 359 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 17 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.104710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080043 restraints weight = 47212.973| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.29 r_work: 0.2987 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4964 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= 0.162 Angle : 0.537 8.736 12432 Z= 0.276 Chirality : 0.040 0.156 1330 Planarity : 0.004 0.069 1613 Dihedral : 4.655 32.019 1201 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.61 % Allowed : 15.48 % Favored : 83.91 % 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: 1.01 (0.26), residues: 1084 helix: 1.84 (0.26), residues: 425 sheet: -0.35 (0.43), residues: 124 loop : 0.04 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 291 HIS 0.002 0.001 HIS A 92 PHE 0.020 0.001 PHE A 344 TYR 0.017 0.001 TYR B 176 ARG 0.014 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10178.00 seconds wall clock time: 180 minutes 14.42 seconds (10814.42 seconds total)