Starting phenix.real_space_refine on Wed Mar 4 03:49:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x21_32954/03_2026/7x21_32954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x21_32954/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x21_32954/03_2026/7x21_32954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x21_32954/03_2026/7x21_32954.map" model { file = "/net/cci-nas-00/data/ceres_data/7x21_32954/03_2026/7x21_32954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x21_32954/03_2026/7x21_32954.cif" } 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-5986/lib/python3.9/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: 11 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: 2.36, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 480.2 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: 0.38 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: 1.99 Time building geometry restraints manager: 1.12 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: 6215 32.98 - 65.96: 140 65.96 - 98.94: 22 98.94 - 131.92: 3 131.92 - 164.91: 1 Dihedral angle restraints: 6381 sinusoidal: 2723 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 6378 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: 1.050 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 14.862 164.905 4022 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 covalent geometry : bond 0.00509 (10349) covalent geometry : angle 1.15302 (14013) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.82633 ( 6) hydrogen bonds : bond 0.14634 ( 475) hydrogen bonds : angle 6.41471 ( 1389) link_NAG-ASN : bond 0.00597 ( 1) link_NAG-ASN : angle 4.61785 ( 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 : 0.372 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: 0.6188 time to fit residues: 100.8878 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 : 0.419 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3926 r_free = 0.3926 target = 0.175929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115028 restraints weight = 11054.935| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.63 r_work: 0.3041 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0955 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= 0.114 Angle : 0.784 29.858 14022 Z= 0.340 Chirality : 0.042 0.287 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.106 163.851 1640 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: 0.62 (0.23), residues: 1259 helix: 1.64 (0.22), residues: 543 sheet: -0.23 (0.40), residues: 147 loop : -0.59 (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 covalent geometry : bond 0.00240 (10349) covalent geometry : angle 0.78301 (14013) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.82771 ( 6) hydrogen bonds : bond 0.04744 ( 475) hydrogen bonds : angle 4.93457 ( 1389) link_NAG-ASN : bond 0.00496 ( 1) link_NAG-ASN : angle 2.87060 ( 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 : 0.410 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0606 (tmm) cc_final: 0.0170 (mpp) REVERT: A 134 ASN cc_start: 0.6059 (m110) cc_final: 0.5751 (m-40) REVERT: A 150 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7463 (tp) REVERT: A 182 LEU cc_start: 0.7407 (tp) cc_final: 0.7205 (tp) REVERT: A 195 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6615 (mt-10) REVERT: A 410 PHE cc_start: 0.6753 (m-80) cc_final: 0.6288 (m-80) REVERT: A 413 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6173 (p0) REVERT: A 500 PHE cc_start: 0.5416 (p90) cc_final: 0.4864 (p90) REVERT: A 534 MET cc_start: 0.6101 (tpp) cc_final: 0.5569 (tpp) REVERT: A 601 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7041 (mp) REVERT: A 651 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: A 963 ARG cc_start: 0.6189 (mtm180) cc_final: 0.5940 (mtt-85) REVERT: B 36 LEU cc_start: 0.7733 (mt) cc_final: 0.7488 (mt) REVERT: B 114 ASP cc_start: 0.6382 (m-30) cc_final: 0.5951 (m-30) REVERT: B 173 LYS cc_start: 0.7349 (mmtp) cc_final: 0.6843 (mptp) REVERT: B 203 MET cc_start: 0.3794 (tpt) cc_final: 0.2616 (mpp) REVERT: B 223 ASP cc_start: 0.6628 (m-30) cc_final: 0.6074 (m-30) REVERT: B 236 PHE cc_start: 0.7059 (m-80) cc_final: 0.6829 (m-80) outliers start: 19 outliers final: 4 residues processed: 145 average time/residue: 0.5691 time to fit residues: 89.2222 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 : 0.365 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3915 r_free = 0.3915 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115774 restraints weight = 11086.378| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.00 r_work: 0.2920 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1143 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= 0.119 Angle : 0.776 29.708 14022 Z= 0.336 Chirality : 0.042 0.249 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.942 171.667 1640 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.12 % Allowed : 9.57 % Favored : 88.32 % 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: 0.59 (0.23), residues: 1259 helix: 1.64 (0.22), residues: 547 sheet: -0.20 (0.40), residues: 148 loop : -0.66 (0.24), residues: 564 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 0.009 0.001 PHE A 405 TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00265 (10349) covalent geometry : angle 0.77476 (14013) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.65565 ( 6) hydrogen bonds : bond 0.04678 ( 475) hydrogen bonds : angle 4.73149 ( 1389) link_NAG-ASN : bond 0.00957 ( 1) link_NAG-ASN : angle 3.19000 ( 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 148 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0784 (tmm) cc_final: 0.0346 (pmm) REVERT: A 134 ASN cc_start: 0.5992 (m110) cc_final: 0.5633 (m-40) REVERT: A 150 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7456 (tp) REVERT: A 182 LEU cc_start: 0.7394 (tp) cc_final: 0.7162 (tp) REVERT: A 195 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6474 (mt-10) REVERT: A 410 PHE cc_start: 0.6693 (m-80) cc_final: 0.6246 (m-80) REVERT: A 500 PHE cc_start: 0.5313 (p90) cc_final: 0.4851 (p90) REVERT: A 534 MET cc_start: 0.6055 (tpp) cc_final: 0.5485 (tpp) REVERT: A 601 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6970 (mp) REVERT: A 603 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: A 651 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.5895 (tp30) REVERT: A 823 ASP cc_start: 0.7373 (m-30) cc_final: 0.7089 (m-30) REVERT: A 963 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5938 (mtt-85) REVERT: B 36 LEU cc_start: 0.7723 (mt) cc_final: 0.7512 (mt) REVERT: B 87 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: B 114 ASP cc_start: 0.6360 (m-30) cc_final: 0.5932 (m-30) REVERT: B 173 LYS cc_start: 0.7324 (mmtp) cc_final: 0.6980 (mptp) REVERT: B 203 MET cc_start: 0.3799 (tpt) cc_final: 0.2620 (mpp) REVERT: B 223 ASP cc_start: 0.6649 (m-30) cc_final: 0.6071 (m-30) REVERT: B 236 PHE cc_start: 0.7067 (m-80) cc_final: 0.6819 (m-80) outliers start: 23 outliers final: 6 residues processed: 136 average time/residue: 0.5503 time to fit residues: 81.1257 Evaluate side-chains 130 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.8980 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.172767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115704 restraints weight = 11141.967| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.89 r_work: 0.2990 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10353 Z= 0.166 Angle : 0.819 30.055 14022 Z= 0.362 Chirality : 0.045 0.271 1597 Planarity : 0.005 0.046 1760 Dihedral : 10.515 176.443 1640 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.58 % Allowed : 11.32 % Favored : 86.11 % 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: 0.43 (0.23), residues: 1259 helix: 1.43 (0.22), residues: 544 sheet: -0.06 (0.40), residues: 141 loop : -0.71 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.023 0.002 TYR A 805 PHE 0.013 0.002 PHE A1021 TRP 0.014 0.002 TRP A 968 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00393 (10349) covalent geometry : angle 0.81803 (14013) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.91719 ( 6) hydrogen bonds : bond 0.05526 ( 475) hydrogen bonds : angle 4.84549 ( 1389) link_NAG-ASN : bond 0.01053 ( 1) link_NAG-ASN : angle 3.11325 ( 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 156 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0380 (tmm) cc_final: 0.0068 (pmm) REVERT: A 107 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6696 (mttp) REVERT: A 150 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 182 LEU cc_start: 0.7484 (tp) cc_final: 0.7260 (tp) REVERT: A 195 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 216 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6291 (tmm160) REVERT: A 500 PHE cc_start: 0.5328 (p90) cc_final: 0.4952 (p90) REVERT: A 534 MET cc_start: 0.6079 (tpp) cc_final: 0.5454 (tpp) REVERT: A 601 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7203 (mp) REVERT: A 603 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7721 (mtt) REVERT: A 651 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6056 (tp30) REVERT: A 823 ASP cc_start: 0.7478 (m-30) cc_final: 0.7270 (m-30) REVERT: A 844 MET cc_start: 0.7836 (mmm) cc_final: 0.7570 (mmm) REVERT: A 963 ARG cc_start: 0.6268 (mtm180) cc_final: 0.6058 (mtt-85) REVERT: B 87 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 114 ASP cc_start: 0.6369 (m-30) cc_final: 0.5952 (m-30) REVERT: B 203 MET cc_start: 0.3704 (tpt) cc_final: 0.2522 (mpp) REVERT: B 213 GLN cc_start: 0.8059 (mt0) cc_final: 0.7786 (mm-40) REVERT: B 223 ASP cc_start: 0.6731 (m-30) cc_final: 0.6163 (m-30) outliers start: 28 outliers final: 12 residues processed: 143 average time/residue: 0.5182 time to fit residues: 80.8498 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 205 ILE Chi-restraints excluded: chain A residue 216 ARG 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 653 VAL 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 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: 5.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 196 GLN A 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.172362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.110647 restraints weight = 11046.506| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.91 r_work: 0.2964 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10353 Z= 0.166 Angle : 0.819 29.880 14022 Z= 0.361 Chirality : 0.045 0.277 1597 Planarity : 0.005 0.047 1760 Dihedral : 10.585 164.605 1640 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.76 % Allowed : 12.05 % Favored : 85.19 % 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: 551 sheet: -0.17 (0.40), residues: 139 loop : -0.70 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 805 PHE 0.014 0.002 PHE A 335 TRP 0.016 0.002 TRP A 968 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00391 (10349) covalent geometry : angle 0.81758 (14013) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.88872 ( 6) hydrogen bonds : bond 0.05453 ( 475) hydrogen bonds : angle 4.82438 ( 1389) link_NAG-ASN : bond 0.01046 ( 1) link_NAG-ASN : angle 3.19856 ( 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 151 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0365 (tmm) cc_final: 0.0103 (pmm) REVERT: A 107 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6743 (mttp) REVERT: A 134 ASN cc_start: 0.6060 (m-40) cc_final: 0.5749 (m-40) REVERT: A 150 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 182 LEU cc_start: 0.7430 (tp) cc_final: 0.7230 (tp) REVERT: A 195 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6610 (mt-10) REVERT: A 216 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6236 (tmm160) REVERT: A 366 LYS cc_start: 0.6766 (mtpt) cc_final: 0.6199 (ptmt) REVERT: A 407 ASN cc_start: 0.6078 (OUTLIER) cc_final: 0.5762 (t0) REVERT: A 500 PHE cc_start: 0.5296 (p90) cc_final: 0.4932 (p90) REVERT: A 502 LEU cc_start: 0.6016 (tp) cc_final: 0.5675 (tm) REVERT: A 534 MET cc_start: 0.5964 (tpp) cc_final: 0.5352 (tpp) REVERT: A 601 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7106 (mp) REVERT: A 603 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: A 651 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6002 (tp30) REVERT: A 844 MET cc_start: 0.7803 (mmm) cc_final: 0.7435 (mmm) REVERT: A 963 ARG cc_start: 0.6267 (mtm180) cc_final: 0.6033 (mtt-85) REVERT: B 87 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: B 114 ASP cc_start: 0.6457 (m-30) cc_final: 0.6074 (m-30) REVERT: B 203 MET cc_start: 0.3688 (tpt) cc_final: 0.2454 (mpp) REVERT: B 223 ASP cc_start: 0.6694 (m-30) cc_final: 0.6137 (m-30) REVERT: B 236 PHE cc_start: 0.7055 (m-80) cc_final: 0.6830 (m-80) REVERT: B 273 ILE cc_start: 0.8128 (mt) cc_final: 0.7786 (mp) outliers start: 30 outliers final: 14 residues processed: 136 average time/residue: 0.5496 time to fit residues: 81.1276 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 407 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3886 r_free = 0.3886 target = 0.172381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115730 restraints weight = 11197.974| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.90 r_work: 0.2985 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10353 Z= 0.171 Angle : 0.823 29.912 14022 Z= 0.364 Chirality : 0.045 0.279 1597 Planarity : 0.005 0.047 1760 Dihedral : 10.715 159.530 1640 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: 0.29 (0.23), residues: 1259 helix: 1.24 (0.22), residues: 551 sheet: -0.20 (0.40), residues: 139 loop : -0.70 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.022 0.002 TYR A 805 PHE 0.013 0.002 PHE A1021 TRP 0.017 0.002 TRP A 968 HIS 0.002 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00403 (10349) covalent geometry : angle 0.82203 (14013) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.89099 ( 6) hydrogen bonds : bond 0.05522 ( 475) hydrogen bonds : angle 4.81672 ( 1389) link_NAG-ASN : bond 0.01056 ( 1) link_NAG-ASN : angle 3.19219 ( 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 153 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0324 (tmm) cc_final: 0.0002 (pmm) REVERT: A 107 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6776 (mttp) REVERT: A 134 ASN cc_start: 0.6198 (m-40) cc_final: 0.5899 (m-40) REVERT: A 150 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7504 (tp) REVERT: A 195 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6602 (mt-10) REVERT: A 216 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6326 (tmm160) REVERT: A 366 LYS cc_start: 0.6817 (mtpt) cc_final: 0.6243 (ptmt) REVERT: A 500 PHE cc_start: 0.5326 (p90) cc_final: 0.4998 (p90) REVERT: A 502 LEU cc_start: 0.6037 (tp) cc_final: 0.5693 (tm) REVERT: A 534 MET cc_start: 0.6032 (tpp) cc_final: 0.5468 (tpp) REVERT: A 601 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7182 (mp) REVERT: A 603 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7579 (mtt) REVERT: A 651 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6088 (tp30) REVERT: A 844 MET cc_start: 0.7705 (mmm) cc_final: 0.7418 (mmm) REVERT: A 963 ARG cc_start: 0.6355 (mtm180) cc_final: 0.6139 (mtt-85) REVERT: B 87 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: B 114 ASP cc_start: 0.6503 (m-30) cc_final: 0.6124 (m-30) REVERT: B 162 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5912 (mt) REVERT: B 203 MET cc_start: 0.3865 (tpt) cc_final: 0.2662 (mpp) REVERT: B 213 GLN cc_start: 0.8078 (mt0) cc_final: 0.7779 (mt0) REVERT: B 223 ASP cc_start: 0.6793 (m-30) cc_final: 0.6223 (m-30) REVERT: B 273 ILE cc_start: 0.8165 (mt) cc_final: 0.7876 (mp) outliers start: 35 outliers final: 17 residues processed: 138 average time/residue: 0.5425 time to fit residues: 81.3546 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 823 ASP 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 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: 2.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3882 r_free = 0.3882 target = 0.172042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114775 restraints weight = 11073.124| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.82 r_work: 0.2985 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10353 Z= 0.180 Angle : 0.834 29.989 14022 Z= 0.370 Chirality : 0.045 0.287 1597 Planarity : 0.005 0.047 1760 Dihedral : 10.794 154.899 1640 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.22 % Allowed : 13.25 % 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: 0.23 (0.23), residues: 1259 helix: 1.17 (0.22), residues: 554 sheet: -0.23 (0.40), residues: 139 loop : -0.73 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.023 0.002 TYR A 805 PHE 0.015 0.002 PHE B 236 TRP 0.018 0.002 TRP A 968 HIS 0.003 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00428 (10349) covalent geometry : angle 0.83280 (14013) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.91123 ( 6) hydrogen bonds : bond 0.05644 ( 475) hydrogen bonds : angle 4.83955 ( 1389) link_NAG-ASN : bond 0.01060 ( 1) link_NAG-ASN : angle 3.21154 ( 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 150 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.310 Fit side-chains REVERT: A 52 MET cc_start: 0.0225 (tmm) cc_final: -0.0067 (pmm) REVERT: A 107 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6758 (mttp) REVERT: A 134 ASN cc_start: 0.6226 (m-40) cc_final: 0.5934 (m-40) REVERT: A 150 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7479 (tp) REVERT: A 195 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 216 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6296 (tmm160) REVERT: A 500 PHE cc_start: 0.5359 (p90) cc_final: 0.5040 (p90) REVERT: A 502 LEU cc_start: 0.6096 (tp) cc_final: 0.5743 (tm) REVERT: A 534 MET cc_start: 0.6093 (tpt) cc_final: 0.5513 (tpp) REVERT: A 601 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7128 (mp) REVERT: A 603 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7590 (mtt) REVERT: A 651 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6090 (tp30) REVERT: B 87 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: B 114 ASP cc_start: 0.6479 (m-30) cc_final: 0.6095 (m-30) REVERT: B 203 MET cc_start: 0.3682 (tpt) cc_final: 0.2508 (mpp) REVERT: B 223 ASP cc_start: 0.6897 (m-30) cc_final: 0.6332 (m-30) REVERT: B 273 ILE cc_start: 0.8175 (mt) cc_final: 0.7874 (mp) outliers start: 35 outliers final: 17 residues processed: 135 average time/residue: 0.5173 time to fit residues: 76.1476 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 : 0.376 ------------------------------------------------------------------------------- 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 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 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 823 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 84 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.175075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114088 restraints weight = 11157.010| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.98 r_work: 0.3013 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10353 Z= 0.108 Angle : 0.775 30.203 14022 Z= 0.334 Chirality : 0.042 0.276 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.195 150.304 1640 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.12 % Allowed : 14.17 % Favored : 83.72 % 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: 0.53 (0.23), residues: 1259 helix: 1.55 (0.22), residues: 550 sheet: -0.27 (0.41), residues: 142 loop : -0.65 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.014 0.001 TYR A 805 PHE 0.011 0.001 PHE A 500 TRP 0.014 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00235 (10349) covalent geometry : angle 0.77210 (14013) SS BOND : bond 0.00448 ( 3) SS BOND : angle 0.65508 ( 6) hydrogen bonds : bond 0.04357 ( 475) hydrogen bonds : angle 4.50939 ( 1389) link_NAG-ASN : bond 0.00307 ( 1) link_NAG-ASN : angle 4.74843 ( 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 142 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.403 Fit side-chains REVERT: A 52 MET cc_start: 0.0081 (tmm) cc_final: -0.0161 (pmm) REVERT: A 107 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6726 (mttp) REVERT: A 134 ASN cc_start: 0.5913 (m-40) cc_final: 0.5571 (m-40) REVERT: A 150 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 195 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6451 (mt-10) REVERT: A 366 LYS cc_start: 0.6811 (mtpt) cc_final: 0.6422 (ptmt) REVERT: A 500 PHE cc_start: 0.5233 (p90) cc_final: 0.4896 (p90) REVERT: A 502 LEU cc_start: 0.5916 (tp) cc_final: 0.5586 (tm) REVERT: A 534 MET cc_start: 0.5853 (tpt) cc_final: 0.5362 (tpp) REVERT: A 601 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6878 (mp) REVERT: A 603 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7305 (mtm) REVERT: A 651 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.5967 (tp30) REVERT: B 114 ASP cc_start: 0.6414 (m-30) cc_final: 0.6057 (m-30) REVERT: B 173 LYS cc_start: 0.7237 (mmtp) cc_final: 0.6783 (mptp) REVERT: B 203 MET cc_start: 0.3821 (tpt) cc_final: 0.2640 (mpp) REVERT: B 213 GLN cc_start: 0.7939 (mt0) cc_final: 0.7699 (mt0) REVERT: B 222 LYS cc_start: 0.6725 (mttp) cc_final: 0.6377 (mttp) REVERT: B 223 ASP cc_start: 0.6730 (m-30) cc_final: 0.6159 (m-30) REVERT: B 273 ILE cc_start: 0.8083 (mt) cc_final: 0.7764 (mp) outliers start: 23 outliers final: 10 residues processed: 133 average time/residue: 0.5368 time to fit residues: 77.5286 Evaluate side-chains 126 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 260 THR 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 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 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: 9.9990 chunk 117 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3903 r_free = 0.3903 target = 0.173800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117475 restraints weight = 11112.960| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.68 r_work: 0.2992 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10353 Z= 0.136 Angle : 0.802 29.660 14022 Z= 0.349 Chirality : 0.043 0.260 1597 Planarity : 0.004 0.043 1760 Dihedral : 10.255 148.940 1640 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.58 % Allowed : 14.26 % 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: 0.49 (0.23), residues: 1259 helix: 1.46 (0.22), residues: 551 sheet: -0.11 (0.42), residues: 128 loop : -0.65 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 397 TYR 0.018 0.002 TYR A 805 PHE 0.011 0.001 PHE A1021 TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00308 (10349) covalent geometry : angle 0.79984 (14013) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.74111 ( 6) hydrogen bonds : bond 0.04894 ( 475) hydrogen bonds : angle 4.59559 ( 1389) link_NAG-ASN : bond 0.01789 ( 1) link_NAG-ASN : angle 3.97902 ( 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 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0083 (tmm) cc_final: -0.0179 (pmm) REVERT: A 107 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6805 (mttp) REVERT: A 134 ASN cc_start: 0.6062 (m-40) cc_final: 0.5695 (m-40) REVERT: A 150 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7467 (tp) REVERT: A 195 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6477 (mt-10) REVERT: A 216 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6329 (tmm160) REVERT: A 366 LYS cc_start: 0.6866 (mtpt) cc_final: 0.6372 (ptmt) REVERT: A 474 VAL cc_start: 0.7181 (OUTLIER) cc_final: 0.6701 (p) REVERT: A 500 PHE cc_start: 0.5294 (p90) cc_final: 0.4997 (p90) REVERT: A 502 LEU cc_start: 0.6077 (tp) cc_final: 0.5732 (tm) REVERT: A 534 MET cc_start: 0.5990 (tpt) cc_final: 0.5490 (tpp) REVERT: A 601 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7018 (mp) REVERT: A 603 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7483 (mtt) REVERT: A 651 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6029 (tp30) REVERT: B 114 ASP cc_start: 0.6478 (m-30) cc_final: 0.6121 (m-30) REVERT: B 203 MET cc_start: 0.3814 (tpt) cc_final: 0.2696 (mpp) REVERT: B 213 GLN cc_start: 0.7973 (mt0) cc_final: 0.7696 (mt0) REVERT: B 223 ASP cc_start: 0.6781 (m-30) cc_final: 0.6211 (m-30) REVERT: B 273 ILE cc_start: 0.8187 (mt) cc_final: 0.7861 (mp) outliers start: 28 outliers final: 13 residues processed: 134 average time/residue: 0.5022 time to fit residues: 73.4787 Evaluate side-chains 130 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 474 VAL 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 806 ILE Chi-restraints excluded: chain A residue 823 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.0030 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118482 restraints weight = 10989.292| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.84 r_work: 0.3004 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1620 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= 0.116 Angle : 0.785 29.932 14022 Z= 0.339 Chirality : 0.042 0.230 1597 Planarity : 0.004 0.042 1760 Dihedral : 9.953 145.758 1640 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.93 % Allowed : 15.18 % Favored : 82.89 % 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: 0.54 (0.23), residues: 1259 helix: 1.54 (0.22), residues: 551 sheet: -0.17 (0.42), residues: 133 loop : -0.66 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 397 TYR 0.015 0.001 TYR A 805 PHE 0.010 0.001 PHE A 445 TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00257 (10349) covalent geometry : angle 0.78352 (14013) SS BOND : bond 0.00328 ( 3) SS BOND : angle 1.05096 ( 6) hydrogen bonds : bond 0.04459 ( 475) hydrogen bonds : angle 4.48368 ( 1389) link_NAG-ASN : bond 0.01388 ( 1) link_NAG-ASN : angle 2.88612 ( 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 135 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0126 (tmm) cc_final: -0.0152 (pmm) REVERT: A 107 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6780 (mttp) REVERT: A 134 ASN cc_start: 0.5852 (m-40) cc_final: 0.5557 (m-40) REVERT: A 150 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7475 (tp) REVERT: A 168 ASN cc_start: 0.4717 (p0) cc_final: 0.4299 (p0) REVERT: A 195 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6462 (mt-10) REVERT: A 216 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6313 (tmm160) REVERT: A 366 LYS cc_start: 0.6763 (mtpt) cc_final: 0.6335 (ptmt) REVERT: A 474 VAL cc_start: 0.7204 (OUTLIER) cc_final: 0.6733 (p) REVERT: A 500 PHE cc_start: 0.5284 (p90) cc_final: 0.4934 (p90) REVERT: A 502 LEU cc_start: 0.6016 (tp) cc_final: 0.5686 (tm) REVERT: A 534 MET cc_start: 0.5892 (tpt) cc_final: 0.5399 (tpp) REVERT: A 601 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6935 (mp) REVERT: A 603 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7457 (mtm) REVERT: A 651 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.5986 (tp30) REVERT: A 823 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7047 (t0) REVERT: B 114 ASP cc_start: 0.6435 (m-30) cc_final: 0.6055 (m-30) REVERT: B 173 LYS cc_start: 0.7188 (mmtp) cc_final: 0.6708 (mptp) REVERT: B 203 MET cc_start: 0.3876 (tpt) cc_final: 0.2684 (mpp) REVERT: B 213 GLN cc_start: 0.7964 (mt0) cc_final: 0.7678 (mt0) REVERT: B 222 LYS cc_start: 0.6818 (mttp) cc_final: 0.6463 (mttp) REVERT: B 223 ASP cc_start: 0.6761 (m-30) cc_final: 0.6183 (m-30) outliers start: 21 outliers final: 11 residues processed: 128 average time/residue: 0.5328 time to fit residues: 74.1648 Evaluate side-chains 128 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 474 VAL 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 806 ILE Chi-restraints excluded: chain A residue 823 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 103 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.174491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114385 restraints weight = 11139.151| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.97 r_work: 0.2978 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1606 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= 0.121 Angle : 0.788 29.689 14022 Z= 0.341 Chirality : 0.042 0.249 1597 Planarity : 0.004 0.043 1760 Dihedral : 9.922 143.621 1640 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.93 % Allowed : 15.27 % Favored : 82.80 % 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: 0.51 (0.23), residues: 1259 helix: 1.51 (0.22), residues: 551 sheet: -0.29 (0.42), residues: 136 loop : -0.63 (0.24), residues: 572 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 0.011 0.001 PHE B 236 TRP 0.009 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00273 (10349) covalent geometry : angle 0.78687 (14013) SS BOND : bond 0.00389 ( 3) SS BOND : angle 0.76127 ( 6) hydrogen bonds : bond 0.04618 ( 475) hydrogen bonds : angle 4.50227 ( 1389) link_NAG-ASN : bond 0.01105 ( 1) link_NAG-ASN : angle 2.85073 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4770.56 seconds wall clock time: 81 minutes 48.28 seconds (4908.28 seconds total)