Starting phenix.real_space_refine on Thu Jul 2 22:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x21_32954/07_2026/7x21_32954.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 6558 2.51 5 N 1651 2.21 5 O 1898 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10167 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7662 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 950} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Unusual residues: {' K': 2, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'NAG': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 1.63, per 1000 atoms: 0.16 Number of scatterers: 10167 At special positions: 0 Unit cell: (122.84, 97.11, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 2 19.00 S 49 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 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 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 366.8 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 48.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.816A pdb=" N GLU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.685A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 139 through 163 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.513A pdb=" N SER A 174 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.728A pdb=" N THR A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 325 Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.971A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 478 through 486 removed outlier: 4.364A pdb=" N ILE A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 610 through 621 removed outlier: 3.546A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.681A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.589A pdb=" N LEU A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 767 through 809 removed outlier: 3.652A pdb=" N ALA A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 removed outlier: 3.642A pdb=" N ILE A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.516A pdb=" N HIS A 868 " --> pdb=" O TYR A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 889 removed outlier: 3.715A pdb=" N MET A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 4.044A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'B' and resid 29 through 59 removed outlier: 3.596A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.127A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.639A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.665A pdb=" N GLY B 157 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 11.892A pdb=" N GLN A 180 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 206 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.615A pdb=" N ASP A 209 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.789A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.682A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 567 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 600 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 565 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 602 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A 563 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.682A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.486A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.775A pdb=" N PHE B 90 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 486 hydrogen bonds defined for protein. 1389 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: 1.68 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3164 1.34 - 1.46: 1518 1.46 - 1.58: 5579 1.58 - 1.70: 6 1.70 - 1.82: 82 Bond restraints: 10349 Sorted by residual: bond pdb=" C11 PCW B 403 " pdb=" O3 PCW B 403 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C11 PCW B 402 " pdb=" O3 PCW B 402 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 PCW B 403 " pdb=" O2 PCW B 403 " ideal model delta sigma weight residual 1.333 1.459 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C31 PCW B 402 " pdb=" O2 PCW B 402 " ideal model delta sigma weight residual 1.333 1.452 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 10344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.12: 14007 14.12 - 28.25: 4 28.25 - 42.37: 0 42.37 - 56.49: 0 56.49 - 70.61: 2 Bond angle restraints: 14013 Sorted by residual: angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.29 -70.61 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.11 -69.48 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 110.21 89.63 20.58 3.00e+00 1.11e-01 4.71e+01 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.69 90.12 19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.59 90.09 19.50 3.00e+00 1.11e-01 4.23e+01 ... (remaining 14008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 6064 32.98 - 65.96: 128 65.96 - 98.94: 22 98.94 - 131.92: 3 131.92 - 164.91: 1 Dihedral angle restraints: 6218 sinusoidal: 2560 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 139.15 -46.15 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" N PCW B 403 " pdb=" C4 PCW B 403 " pdb=" C5 PCW B 403 " pdb=" O4P PCW B 403 " ideal model delta sinusoidal sigma weight residual -66.66 98.25 -164.91 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA PHE B 296 " pdb=" C PHE B 296 " pdb=" N ASP B 297 " pdb=" CA ASP B 297 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1386 0.064 - 0.129: 200 0.129 - 0.193: 5 0.193 - 0.257: 3 0.257 - 0.321: 3 Chirality restraints: 1597 Sorted by residual: chirality pdb=" C2 PCW A1106 " pdb=" C1 PCW A1106 " pdb=" C3 PCW A1106 " pdb=" O2 PCW A1106 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 PCW B 402 " pdb=" C1 PCW B 402 " pdb=" C3 PCW B 402 " pdb=" O2 PCW B 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.60 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1594 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.277 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C7 NAG B 401 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1029 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TRP A1029 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP A1029 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A1030 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 891 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO A 892 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " -0.030 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 74 2.58 - 3.22: 9709 3.22 - 3.86: 20075 3.86 - 4.50: 27689 4.50 - 5.14: 43956 Nonbonded interactions: 101503 Sorted by model distance: nonbonded pdb=" F3 ALF A1103 " pdb="MG MG A1104 " model vdw 1.943 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1104 " model vdw 2.066 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1104 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 823 " pdb=" O HOH A1201 " model vdw 2.142 3.040 nonbonded pdb=" OG SER A 955 " pdb=" OE1 GLU A1016 " model vdw 2.171 3.040 ... (remaining 101498 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: 0.960 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.005 0.128 10353 Z= 0.247 Angle : 1.155 70.615 14022 Z= 0.452 Chirality : 0.046 0.321 1597 Planarity : 0.007 0.232 1760 Dihedral : 14.804 164.905 3859 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.45 (0.23), residues: 1259 helix: 1.48 (0.22), residues: 527 sheet: -0.06 (0.41), residues: 140 loop : -0.67 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 397 TYR 0.017 0.002 TYR A 257 PHE 0.020 0.002 PHE B 236 TRP 0.019 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.25 (10349) covalent geometry : angle 1.15302 / 0.45 (14013) SS BOND : bond 0.00217 / 0.12 ( 3) SS BOND : angle 0.82633 / 0.34 ( 6) hydrogen bonds : bond 0.14634 / 9.60 ( 475) hydrogen bonds : angle 6.41471 / 4.57 ( 1389) link_NAG-ASN : bond 0.00597 / 0.37 ( 1) link_NAG-ASN : angle 4.61785 / 1.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0606 (tmm) cc_final: 0.0140 (mpp) REVERT: A 71 ASN cc_start: 0.6290 (t0) cc_final: 0.5696 (t0) REVERT: A 195 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6393 (mt-10) REVERT: A 366 LYS cc_start: 0.6567 (mtmt) cc_final: 0.6322 (mtpt) REVERT: A 500 PHE cc_start: 0.5418 (p90) cc_final: 0.4792 (p90) REVERT: A 911 GLU cc_start: 0.7372 (tt0) cc_final: 0.7160 (tt0) REVERT: B 36 LEU cc_start: 0.7676 (mt) cc_final: 0.7475 (mt) REVERT: B 63 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 114 ASP cc_start: 0.6179 (m-30) cc_final: 0.5694 (m-30) REVERT: B 203 MET cc_start: 0.3649 (tpt) cc_final: 0.2479 (mpp) REVERT: B 223 ASP cc_start: 0.6622 (m-30) cc_final: 0.6194 (m-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4854 time to fit residues: 79.3614 Evaluate side-chains 120 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 732 ASN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.175969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115103 restraints weight = 11054.087| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.63 r_work: 0.3045 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10353 Z= 0.114 Angle : 0.785 29.882 14022 Z= 0.341 Chirality : 0.042 0.280 1597 Planarity : 0.004 0.043 1760 Dihedral : 9.661 154.666 1477 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.75 % Allowed : 7.18 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.61 (0.23), residues: 1259 helix: 1.64 (0.22), residues: 543 sheet: -0.23 (0.40), residues: 147 loop : -0.60 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.016 0.001 TYR A 881 PHE 0.011 0.001 PHE A 335 TRP 0.013 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10349) covalent geometry : angle 0.78389 / 0.34 (14013) SS BOND : bond 0.00145 / 0.08 ( 3) SS BOND : angle 0.80260 / 0.39 ( 6) hydrogen bonds : bond 0.04708 / 3.14 ( 475) hydrogen bonds : angle 4.92448 / 3.47 ( 1389) link_NAG-ASN : bond 0.00315 / 0.20 ( 1) link_NAG-ASN : angle 2.86297 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0602 (tmm) cc_final: 0.0171 (mpp) REVERT: A 134 ASN cc_start: 0.6057 (m110) cc_final: 0.5746 (m-40) REVERT: A 150 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 182 LEU cc_start: 0.7398 (tp) cc_final: 0.7196 (tp) REVERT: A 195 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6608 (mt-10) REVERT: A 410 PHE cc_start: 0.6764 (m-80) cc_final: 0.6296 (m-80) REVERT: A 413 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6181 (p0) REVERT: A 500 PHE cc_start: 0.5403 (p90) cc_final: 0.4850 (p90) REVERT: A 534 MET cc_start: 0.6091 (tpp) cc_final: 0.5560 (tpp) REVERT: A 601 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7060 (mp) REVERT: A 651 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.5890 (tp30) REVERT: A 963 ARG cc_start: 0.6184 (mtm180) cc_final: 0.5934 (mtt-85) REVERT: B 36 LEU cc_start: 0.7732 (mt) cc_final: 0.7484 (mt) REVERT: B 114 ASP cc_start: 0.6381 (m-30) cc_final: 0.5951 (m-30) REVERT: B 173 LYS cc_start: 0.7350 (mmtp) cc_final: 0.6844 (mptp) REVERT: B 203 MET cc_start: 0.3797 (tpt) cc_final: 0.2615 (mpp) REVERT: B 223 ASP cc_start: 0.6620 (m-30) cc_final: 0.6067 (m-30) REVERT: B 236 PHE cc_start: 0.7046 (m-80) cc_final: 0.6817 (m-80) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.4206 time to fit residues: 66.1612 Evaluate side-chains 128 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 846 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.0040 chunk 91 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN B 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119558 restraints weight = 11075.950| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.64 r_work: 0.3025 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10353 Z= 0.116 Angle : 0.775 29.773 14022 Z= 0.334 Chirality : 0.042 0.246 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.279 160.893 1477 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.12 % Allowed : 9.66 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.61 (0.23), residues: 1259 helix: 1.65 (0.22), residues: 547 sheet: -0.20 (0.40), residues: 148 loop : -0.64 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.015 0.001 TYR A 881 PHE 0.009 0.001 PHE A 935 TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10349) covalent geometry : angle 0.77325 / 0.33 (14013) SS BOND : bond 0.00279 / 0.15 ( 3) SS BOND : angle 0.65826 / 0.26 ( 6) hydrogen bonds : bond 0.04622 / 3.08 ( 475) hydrogen bonds : angle 4.70112 / 3.30 ( 1389) link_NAG-ASN : bond 0.00954 / 0.60 ( 1) link_NAG-ASN : angle 3.31963 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0680 (tmm) cc_final: 0.0356 (pmm) REVERT: A 134 ASN cc_start: 0.6029 (m110) cc_final: 0.5668 (m-40) REVERT: A 150 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7522 (tp) REVERT: A 182 LEU cc_start: 0.7509 (tp) cc_final: 0.7262 (tp) REVERT: A 195 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6568 (mt-10) REVERT: A 410 PHE cc_start: 0.6756 (m-80) cc_final: 0.6340 (m-80) REVERT: A 500 PHE cc_start: 0.5375 (p90) cc_final: 0.4926 (p90) REVERT: A 534 MET cc_start: 0.6115 (tpp) cc_final: 0.5551 (tpp) REVERT: A 601 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7039 (mp) REVERT: A 603 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7467 (mtt) REVERT: A 651 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6003 (tp30) REVERT: A 823 ASP cc_start: 0.7436 (m-30) cc_final: 0.7144 (m-30) REVERT: A 963 ARG cc_start: 0.6227 (mtm180) cc_final: 0.5970 (mtt-85) REVERT: B 36 LEU cc_start: 0.7793 (mt) cc_final: 0.7588 (mt) REVERT: B 87 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: B 114 ASP cc_start: 0.6401 (m-30) cc_final: 0.5974 (m-30) REVERT: B 173 LYS cc_start: 0.7378 (mmtp) cc_final: 0.7028 (mptp) REVERT: B 203 MET cc_start: 0.3781 (tpt) cc_final: 0.2622 (mpp) REVERT: B 222 LYS cc_start: 0.6774 (mttp) cc_final: 0.6476 (mttp) REVERT: B 223 ASP cc_start: 0.6711 (m-30) cc_final: 0.6133 (m-30) outliers start: 23 outliers final: 6 residues processed: 141 average time/residue: 0.4218 time to fit residues: 64.8479 Evaluate side-chains 129 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 87 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.174056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117600 restraints weight = 11154.596| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.80 r_work: 0.3024 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10353 Z= 0.133 Angle : 0.786 29.703 14022 Z= 0.341 Chirality : 0.043 0.253 1597 Planarity : 0.004 0.044 1760 Dihedral : 9.423 166.589 1477 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.58 % Allowed : 11.22 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.60 (0.23), residues: 1259 helix: 1.57 (0.22), residues: 548 sheet: -0.00 (0.41), residues: 141 loop : -0.62 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.018 0.002 TYR A 805 PHE 0.013 0.001 PHE B 236 TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10349) covalent geometry : angle 0.78467 / 0.34 (14013) SS BOND : bond 0.00270 / 0.15 ( 3) SS BOND : angle 0.76175 / 0.30 ( 6) hydrogen bonds : bond 0.04885 / 3.25 ( 475) hydrogen bonds : angle 4.67578 / 3.28 ( 1389) link_NAG-ASN : bond 0.00955 / 0.60 ( 1) link_NAG-ASN : angle 3.26156 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0501 (tmm) cc_final: 0.0152 (pmm) REVERT: A 107 LYS cc_start: 0.7227 (mptp) cc_final: 0.6760 (mttp) REVERT: A 134 ASN cc_start: 0.6064 (m110) cc_final: 0.5697 (m-40) REVERT: A 150 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7503 (tp) REVERT: A 182 LEU cc_start: 0.7503 (tp) cc_final: 0.7259 (tp) REVERT: A 195 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 500 PHE cc_start: 0.5312 (p90) cc_final: 0.4813 (p90) REVERT: A 534 MET cc_start: 0.6029 (tpp) cc_final: 0.5463 (tpp) REVERT: A 601 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7100 (mp) REVERT: A 603 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7517 (mtt) REVERT: A 651 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: A 823 ASP cc_start: 0.7406 (m-30) cc_final: 0.7170 (m-30) REVERT: A 963 ARG cc_start: 0.6213 (mtm180) cc_final: 0.6009 (mtt-85) REVERT: B 87 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 114 ASP cc_start: 0.6329 (m-30) cc_final: 0.5915 (m-30) REVERT: B 173 LYS cc_start: 0.7378 (mmtp) cc_final: 0.6978 (mptp) REVERT: B 203 MET cc_start: 0.3744 (tpt) cc_final: 0.2535 (mpp) REVERT: B 213 GLN cc_start: 0.8041 (mt0) cc_final: 0.7788 (mt0) REVERT: B 222 LYS cc_start: 0.6723 (mttp) cc_final: 0.6368 (mttp) REVERT: B 223 ASP cc_start: 0.6731 (m-30) cc_final: 0.6165 (m-30) REVERT: B 236 PHE cc_start: 0.7124 (m-80) cc_final: 0.6874 (m-80) outliers start: 28 outliers final: 12 residues processed: 138 average time/residue: 0.5444 time to fit residues: 81.4340 Evaluate side-chains 134 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119005 restraints weight = 11049.840| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.89 r_work: 0.3009 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10353 Z= 0.118 Angle : 0.771 29.732 14022 Z= 0.332 Chirality : 0.042 0.253 1597 Planarity : 0.004 0.043 1760 Dihedral : 9.359 169.638 1477 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.85 % Allowed : 11.32 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.66 (0.23), residues: 1259 helix: 1.64 (0.22), residues: 548 sheet: -0.10 (0.41), residues: 143 loop : -0.58 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.016 0.001 TYR A 805 PHE 0.014 0.001 PHE A 335 TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10349) covalent geometry : angle 0.76975 / 0.33 (14013) SS BOND : bond 0.00228 / 0.13 ( 3) SS BOND : angle 0.71471 / 0.27 ( 6) hydrogen bonds : bond 0.04577 / 3.05 ( 475) hydrogen bonds : angle 4.55818 / 3.20 ( 1389) link_NAG-ASN : bond 0.01018 / 0.64 ( 1) link_NAG-ASN : angle 3.36291 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0431 (tmm) cc_final: 0.0148 (pmm) REVERT: A 107 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6772 (mttp) REVERT: A 134 ASN cc_start: 0.6088 (m110) cc_final: 0.5674 (m-40) REVERT: A 150 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7524 (tp) REVERT: A 182 LEU cc_start: 0.7500 (tp) cc_final: 0.7257 (tp) REVERT: A 195 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 216 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6359 (tmm160) REVERT: A 366 LYS cc_start: 0.6773 (mtpt) cc_final: 0.6248 (ptmt) REVERT: A 410 PHE cc_start: 0.6764 (m-80) cc_final: 0.6450 (m-80) REVERT: A 500 PHE cc_start: 0.5272 (p90) cc_final: 0.4883 (p90) REVERT: A 534 MET cc_start: 0.5985 (tpp) cc_final: 0.5429 (tpp) REVERT: A 601 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 603 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7468 (mtt) REVERT: A 651 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6010 (tp30) REVERT: A 823 ASP cc_start: 0.7444 (m-30) cc_final: 0.7183 (m-30) REVERT: A 963 ARG cc_start: 0.6220 (mtm180) cc_final: 0.5768 (mtt90) REVERT: B 114 ASP cc_start: 0.6415 (m-30) cc_final: 0.6022 (m-30) REVERT: B 173 LYS cc_start: 0.7278 (mmtp) cc_final: 0.6834 (mptp) REVERT: B 203 MET cc_start: 0.3600 (tpt) cc_final: 0.2474 (mpp) REVERT: B 213 GLN cc_start: 0.8052 (mt0) cc_final: 0.7779 (mm-40) REVERT: B 222 LYS cc_start: 0.6679 (mttp) cc_final: 0.6313 (mttp) REVERT: B 223 ASP cc_start: 0.6748 (m-30) cc_final: 0.6184 (m-30) outliers start: 31 outliers final: 14 residues processed: 141 average time/residue: 0.5057 time to fit residues: 77.4911 Evaluate side-chains 140 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 0.0770 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114451 restraints weight = 11176.880| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.71 r_work: 0.2945 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10353 Z= 0.222 Angle : 0.871 30.660 14022 Z= 0.392 Chirality : 0.047 0.289 1597 Planarity : 0.005 0.053 1760 Dihedral : 10.412 170.387 1477 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.22 % Allowed : 12.33 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.15 (0.23), residues: 1259 helix: 1.06 (0.22), residues: 557 sheet: -0.19 (0.41), residues: 129 loop : -0.75 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 397 TYR 0.029 0.002 TYR A 805 PHE 0.018 0.002 PHE A1021 TRP 0.015 0.002 TRP A 968 HIS 0.004 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (10349) covalent geometry : angle 0.87011 / 0.39 (14013) SS BOND : bond 0.00424 / 0.25 ( 3) SS BOND : angle 1.06318 / 0.47 ( 6) hydrogen bonds : bond 0.06251 / 4.15 ( 475) hydrogen bonds : angle 4.96548 / 3.50 ( 1389) link_NAG-ASN : bond 0.01002 / 0.63 ( 1) link_NAG-ASN : angle 3.08306 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0337 (tmm) cc_final: 0.0035 (pmm) REVERT: A 107 LYS cc_start: 0.7205 (mptp) cc_final: 0.6714 (mttp) REVERT: A 150 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 179 GLN cc_start: 0.6065 (mp10) cc_final: 0.5823 (mp10) REVERT: A 195 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 216 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6290 (tmm160) REVERT: A 500 PHE cc_start: 0.5337 (p90) cc_final: 0.5008 (p90) REVERT: A 502 LEU cc_start: 0.5966 (tp) cc_final: 0.5630 (tm) REVERT: A 534 MET cc_start: 0.6085 (tpt) cc_final: 0.5495 (tpp) REVERT: A 601 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 603 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7701 (mtt) REVERT: A 651 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6117 (tp30) REVERT: A 823 ASP cc_start: 0.7533 (m-30) cc_final: 0.7326 (m-30) REVERT: A 844 MET cc_start: 0.7783 (mmm) cc_final: 0.7413 (mmm) REVERT: A 963 ARG cc_start: 0.6347 (mtm180) cc_final: 0.6128 (mtt-85) REVERT: B 114 ASP cc_start: 0.6507 (m-30) cc_final: 0.6119 (m-30) REVERT: B 162 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5943 (mt) REVERT: B 203 MET cc_start: 0.3822 (tpt) cc_final: 0.2619 (mpp) REVERT: B 223 ASP cc_start: 0.6776 (m-30) cc_final: 0.6219 (m-30) REVERT: B 273 ILE cc_start: 0.8175 (mt) cc_final: 0.7865 (mp) outliers start: 35 outliers final: 17 residues processed: 140 average time/residue: 0.4640 time to fit residues: 70.7070 Evaluate side-chains 141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 118 optimal weight: 0.0050 chunk 41 optimal weight: 7.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114503 restraints weight = 11072.420| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.89 r_work: 0.2948 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10353 Z= 0.158 Angle : 0.816 29.901 14022 Z= 0.360 Chirality : 0.044 0.283 1597 Planarity : 0.004 0.045 1760 Dihedral : 10.213 163.424 1477 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.04 % Allowed : 12.88 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.33 (0.23), residues: 1259 helix: 1.28 (0.22), residues: 549 sheet: -0.10 (0.41), residues: 136 loop : -0.71 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.022 0.002 TYR A 805 PHE 0.012 0.002 PHE A1021 TRP 0.015 0.002 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10349) covalent geometry : angle 0.81422 / 0.36 (14013) SS BOND : bond 0.00313 / 0.18 ( 3) SS BOND : angle 0.82618 / 0.35 ( 6) hydrogen bonds : bond 0.05364 / 3.56 ( 475) hydrogen bonds : angle 4.78337 / 3.37 ( 1389) link_NAG-ASN : bond 0.01089 / 0.68 ( 1) link_NAG-ASN : angle 3.22881 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0260 (tmm) cc_final: 0.0004 (pmm) REVERT: A 107 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6647 (mttp) REVERT: A 150 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7447 (tp) REVERT: A 195 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 216 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6295 (tmm160) REVERT: A 366 LYS cc_start: 0.6804 (mtpt) cc_final: 0.6231 (ptmt) REVERT: A 500 PHE cc_start: 0.5292 (p90) cc_final: 0.4943 (p90) REVERT: A 502 LEU cc_start: 0.5939 (tp) cc_final: 0.5601 (tm) REVERT: A 534 MET cc_start: 0.5964 (tpt) cc_final: 0.5417 (tpp) REVERT: A 601 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7095 (mp) REVERT: A 603 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: A 651 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6077 (tp30) REVERT: A 823 ASP cc_start: 0.7473 (m-30) cc_final: 0.7261 (m-30) REVERT: A 844 MET cc_start: 0.7683 (mmm) cc_final: 0.7305 (mmm) REVERT: A 845 ASN cc_start: 0.7114 (m-40) cc_final: 0.6902 (m110) REVERT: A 963 ARG cc_start: 0.6293 (mtm180) cc_final: 0.6039 (mtt-85) REVERT: B 87 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 114 ASP cc_start: 0.6492 (m-30) cc_final: 0.6111 (m-30) REVERT: B 203 MET cc_start: 0.3846 (tpt) cc_final: 0.2636 (mpp) REVERT: B 213 GLN cc_start: 0.8067 (mt0) cc_final: 0.7763 (mt0) REVERT: B 223 ASP cc_start: 0.6848 (m-30) cc_final: 0.6288 (m-30) REVERT: B 273 ILE cc_start: 0.8166 (mt) cc_final: 0.7857 (mp) outliers start: 33 outliers final: 17 residues processed: 138 average time/residue: 0.4668 time to fit residues: 69.8660 Evaluate side-chains 138 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.174347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117169 restraints weight = 11108.731| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.95 r_work: 0.2985 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10353 Z= 0.115 Angle : 0.775 29.968 14022 Z= 0.335 Chirality : 0.042 0.260 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.694 158.379 1477 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.48 % Allowed : 13.62 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.57 (0.23), residues: 1259 helix: 1.52 (0.22), residues: 552 sheet: -0.06 (0.42), residues: 128 loop : -0.60 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.016 0.001 TYR A 805 PHE 0.010 0.001 PHE A 500 TRP 0.013 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (10349) covalent geometry : angle 0.77405 / 0.33 (14013) SS BOND : bond 0.00229 / 0.13 ( 3) SS BOND : angle 0.62848 / 0.26 ( 6) hydrogen bonds : bond 0.04544 / 3.04 ( 475) hydrogen bonds : angle 4.55125 / 3.20 ( 1389) link_NAG-ASN : bond 0.01019 / 0.64 ( 1) link_NAG-ASN : angle 3.39309 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0188 (tmm) cc_final: -0.0103 (pmm) REVERT: A 107 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6652 (mttp) REVERT: A 150 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7464 (tp) REVERT: A 195 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6538 (mt-10) REVERT: A 216 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6276 (tmm160) REVERT: A 366 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6280 (ptmt) REVERT: A 500 PHE cc_start: 0.5196 (p90) cc_final: 0.4842 (p90) REVERT: A 502 LEU cc_start: 0.6027 (tp) cc_final: 0.5683 (tm) REVERT: A 534 MET cc_start: 0.5825 (tpt) cc_final: 0.5327 (tpp) REVERT: A 601 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7008 (mp) REVERT: A 603 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: A 651 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: A 823 ASP cc_start: 0.7466 (m-30) cc_final: 0.7220 (m-30) REVERT: A 844 MET cc_start: 0.7669 (mmm) cc_final: 0.7337 (mmm) REVERT: A 845 ASN cc_start: 0.7144 (m-40) cc_final: 0.6935 (m110) REVERT: A 963 ARG cc_start: 0.6295 (mtm180) cc_final: 0.5850 (mtt90) REVERT: B 87 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 114 ASP cc_start: 0.6458 (m-30) cc_final: 0.6092 (m-30) REVERT: B 173 LYS cc_start: 0.7242 (mmtp) cc_final: 0.6789 (mptp) REVERT: B 203 MET cc_start: 0.3814 (tpt) cc_final: 0.2668 (mpp) REVERT: B 213 GLN cc_start: 0.7980 (mt0) cc_final: 0.7694 (mt0) REVERT: B 222 LYS cc_start: 0.6691 (mttp) cc_final: 0.6269 (mttp) REVERT: B 223 ASP cc_start: 0.6732 (m-30) cc_final: 0.6155 (m-30) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.5377 time to fit residues: 76.9518 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.172421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112873 restraints weight = 11024.963| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.83 r_work: 0.2953 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10353 Z= 0.168 Angle : 0.826 30.052 14022 Z= 0.365 Chirality : 0.045 0.274 1597 Planarity : 0.004 0.046 1760 Dihedral : 9.984 156.056 1477 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.85 % Allowed : 13.52 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.39 (0.23), residues: 1259 helix: 1.33 (0.22), residues: 549 sheet: -0.14 (0.42), residues: 128 loop : -0.66 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.022 0.002 TYR A 805 PHE 0.013 0.002 PHE A1021 TRP 0.012 0.002 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (10349) covalent geometry : angle 0.82423 / 0.36 (14013) SS BOND : bond 0.00294 / 0.17 ( 3) SS BOND : angle 0.83734 / 0.35 ( 6) hydrogen bonds : bond 0.05448 / 3.62 ( 475) hydrogen bonds : angle 4.73159 / 3.32 ( 1389) link_NAG-ASN : bond 0.00983 / 0.61 ( 1) link_NAG-ASN : angle 3.24027 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.246 Fit side-chains REVERT: A 52 MET cc_start: 0.0091 (tmm) cc_final: -0.0146 (pmm) REVERT: A 107 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6689 (mttp) REVERT: A 134 ASN cc_start: 0.5975 (m-40) cc_final: 0.5701 (m-40) REVERT: A 150 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7490 (tp) REVERT: A 195 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6524 (mt-10) REVERT: A 216 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6272 (tmm160) REVERT: A 366 LYS cc_start: 0.6826 (mtpt) cc_final: 0.6269 (ptmt) REVERT: A 500 PHE cc_start: 0.5224 (p90) cc_final: 0.4915 (p90) REVERT: A 502 LEU cc_start: 0.6050 (tp) cc_final: 0.5708 (tm) REVERT: A 534 MET cc_start: 0.5970 (tpt) cc_final: 0.5442 (tpp) REVERT: A 601 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7083 (mp) REVERT: A 603 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7593 (mtt) REVERT: A 651 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6054 (tp30) REVERT: A 823 ASP cc_start: 0.7453 (m-30) cc_final: 0.7215 (m-30) REVERT: A 845 ASN cc_start: 0.7126 (m-40) cc_final: 0.6891 (m110) REVERT: B 87 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: B 114 ASP cc_start: 0.6468 (m-30) cc_final: 0.6094 (m-30) REVERT: B 203 MET cc_start: 0.3863 (tpt) cc_final: 0.2713 (mpp) REVERT: B 223 ASP cc_start: 0.6810 (m-30) cc_final: 0.6246 (m-30) REVERT: B 273 ILE cc_start: 0.8135 (mt) cc_final: 0.7823 (mp) outliers start: 31 outliers final: 16 residues processed: 138 average time/residue: 0.4312 time to fit residues: 65.1373 Evaluate side-chains 138 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN B 208 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.174638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115637 restraints weight = 10923.910| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.69 r_work: 0.2993 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10353 Z= 0.113 Angle : 0.780 30.121 14022 Z= 0.337 Chirality : 0.042 0.191 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.563 157.147 1477 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.12 % Allowed : 14.35 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.57 (0.23), residues: 1259 helix: 1.53 (0.22), residues: 553 sheet: -0.18 (0.42), residues: 133 loop : -0.60 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.016 0.001 TYR A 805 PHE 0.023 0.001 PHE A 335 TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10349) covalent geometry : angle 0.77924 / 0.34 (14013) SS BOND : bond 0.00234 / 0.13 ( 3) SS BOND : angle 0.67814 / 0.30 ( 6) hydrogen bonds : bond 0.04486 / 3.00 ( 475) hydrogen bonds : angle 4.52523 / 3.17 ( 1389) link_NAG-ASN : bond 0.00680 / 0.43 ( 1) link_NAG-ASN : angle 2.09511 / 0.96 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.477 Fit side-chains REVERT: A 52 MET cc_start: 0.0110 (tmm) cc_final: -0.0133 (pmm) REVERT: A 107 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6719 (mttp) REVERT: A 150 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7526 (tp) REVERT: A 195 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6500 (mt-10) REVERT: A 216 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6337 (tmm160) REVERT: A 366 LYS cc_start: 0.6785 (mtpt) cc_final: 0.6349 (ptmt) REVERT: A 500 PHE cc_start: 0.5242 (p90) cc_final: 0.4918 (p90) REVERT: A 502 LEU cc_start: 0.6027 (tp) cc_final: 0.5692 (tm) REVERT: A 534 MET cc_start: 0.5862 (tpt) cc_final: 0.5386 (tpp) REVERT: A 601 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 603 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7490 (mtt) REVERT: A 651 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6028 (tp30) REVERT: A 823 ASP cc_start: 0.7500 (m-30) cc_final: 0.7234 (m-30) REVERT: A 845 ASN cc_start: 0.7127 (m-40) cc_final: 0.6924 (m110) REVERT: A 963 ARG cc_start: 0.6329 (mtm180) cc_final: 0.5860 (mtt90) REVERT: B 114 ASP cc_start: 0.6468 (m-30) cc_final: 0.6105 (m-30) REVERT: B 173 LYS cc_start: 0.7294 (mmtp) cc_final: 0.6831 (mptp) REVERT: B 203 MET cc_start: 0.3896 (tpt) cc_final: 0.2750 (mpp) REVERT: B 213 GLN cc_start: 0.8044 (mt0) cc_final: 0.7786 (mt0) REVERT: B 222 LYS cc_start: 0.6808 (mttp) cc_final: 0.6364 (mttp) REVERT: B 223 ASP cc_start: 0.6768 (m-30) cc_final: 0.6192 (m-30) outliers start: 23 outliers final: 14 residues processed: 132 average time/residue: 0.4830 time to fit residues: 69.5389 Evaluate side-chains 133 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 417 ASN B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.174985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113827 restraints weight = 11077.982| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.01 r_work: 0.3001 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10353 Z= 0.112 Angle : 0.781 29.789 14022 Z= 0.336 Chirality : 0.042 0.165 1597 Planarity : 0.004 0.041 1760 Dihedral : 9.373 154.963 1477 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.12 % Allowed : 14.72 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.60 (0.23), residues: 1259 helix: 1.59 (0.22), residues: 551 sheet: -0.18 (0.42), residues: 133 loop : -0.60 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.015 0.001 TYR A 805 PHE 0.020 0.001 PHE A 335 TRP 0.010 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10349) covalent geometry : angle 0.77898 / 0.34 (14013) SS BOND : bond 0.00108 / 0.06 ( 3) SS BOND : angle 0.70528 / 0.32 ( 6) hydrogen bonds : bond 0.04415 / 2.95 ( 475) hydrogen bonds : angle 4.44960 / 3.12 ( 1389) link_NAG-ASN : bond 0.00445 / 0.28 ( 1) link_NAG-ASN : angle 3.72044 / 1.92 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4079.54 seconds wall clock time: 70 minutes 0.80 seconds (4200.80 seconds total)